MotifMatch error in wbc19-aluru.R

[thardy615]

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

[paul-shannon]

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon notifications@github.com wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

Yes, please. So I have exactly the same code and data as you. Then tell me exactly what to do to see your error.

(Good to hear from you!)

On Sep 10, 2019, at 6:28 PM, thardy615 notifications@github.com wrote:

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon notifications@github.com wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[paul-shannon]

Hi Tanjanay,

I am not yet able to reproduce your error here.

Could you try two things, please?

Create a tiny example script which reproduces the error. inst/sgm/wbc19-alaru.R is > 2000 lines! When you start R, type:

R> sessionInfo()

and send me the output. This tells us the version of every package you are using.

Thank you! We should be able to fix this quick.

• Paul

On Sep 10, 2019, at 6:29 PM, Paul Shannon notifications@github.com wrote:

Yes, please. So I have exactly the same code and data as you. Then tell me exactly what to do to see your error.

(Good to hear from you!)

On Sep 10, 2019, at 6:28 PM, thardy615 notifications@github.com wrote:

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon notifications@github.com wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[paul-shannon]

@thardy615

trena’s MotifMatcher supports tair10 since at least Version: 1.7.7, 2019-08-10. So maybe you have an out-of-date version?

sessionInfo() should tell us all we need to know.

• Paul

On Sep 11, 2019, at 5:18 AM, Paul Shannon notifications@github.com wrote:

Hi Tanjanay,

I am not yet able to reproduce your error here.

Could you try two things, please?

Create a tiny example script which reproduces the error. inst/sgm/wbc19-alaru.R is > 2000 lines! When you start R, type:

R> sessionInfo()

and send me the output. This tells us the version of every package you are using.

Thank you! We should be able to fix this quick.

• Paul

On Sep 10, 2019, at 6:29 PM, Paul Shannon notifications@github.com wrote:

Yes, please. So I have exactly the same code and data as you. Then tell me exactly what to do to see your error.

(Good to hear from you!)

On Sep 10, 2019, at 6:28 PM, thardy615 notifications@github.com wrote:

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon notifications@github.com wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

I sourced the file I recently pushed on GitHub and got the same error message: " > source('~/github/TrenaProjectArabidopsisRoot/explore/networks/v1/trenaModel.1.WBC19.R') Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'"

I used sessionInfo() and saw that the version for MotifDb is 1.26. I remember back at ISB I had the same issue with getting the updated version for a package and i solved it by installing it from a different branch other than the "master" branch. Is that the case for MotifDb or another package?

On Wed, Sep 11, 2019 at 8:30 AM Paul Shannon notifications@github.com wrote:

@thardy615

trena’s MotifMatcher supports tair10 since at least Version: 1.7.7, 2019-08-10. So maybe you have an out-of-date version?

sessionInfo() should tell us all we need to know.

• Paul

On Sep 11, 2019, at 5:18 AM, Paul Shannon notifications@github.com wrote:

Hi Tanjanay,

I am not yet able to reproduce your error here.

Could you try two things, please?

Create a tiny example script which reproduces the error. inst/sgm/wbc19-alaru.R is > 2000 lines! When you start R, type:

R> sessionInfo()

and send me the output. This tells us the version of every package you are using.

Thank you! We should be able to fix this quick.

• Paul

On Sep 10, 2019, at 6:29 PM, Paul Shannon notifications@github.com wrote:

Yes, please. So I have exactly the same code and data as you. Then tell me exactly what to do to see your error.

(Good to hear from you!)

On Sep 10, 2019, at 6:28 PM, thardy615 notifications@github.com wrote:

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon < notifications@github.com> wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ

.

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7SHD6OUFIEQA2GWOVDQJDQFXA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6OKBMA#issuecomment-530358448, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7X4JQ2W7C33YYJ5LRTQJDQFXANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

Please send ALL (!) of the output of sessionInfo(). You likely have an out-of-date version of the trena package.

MotifDb should not be a problem. I’ll bet you a dollar!

On Sep 11, 2019, at 9:55 AM, thardy615 notifications@github.com wrote:

I sourced the file I recently pushed on GitHub and got the same error message: " > source('~/github/TrenaProjectArabidopsisRoot/explore/networks/v1/trenaModel.1.WBC19.R') Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'"

I used sessionInfo() and saw that the version for MotifDb is 1.26. I remember back at ISB I had the same issue with getting the updated version for a package and i solved it by installing it from a different branch other than the "master" branch. Is that the case for MotifDb or another package?

On Wed, Sep 11, 2019 at 8:30 AM Paul Shannon notifications@github.com wrote:

@thardy615

trena’s MotifMatcher supports tair10 since at least Version: 1.7.7, 2019-08-10. So maybe you have an out-of-date version?

sessionInfo() should tell us all we need to know.

• Paul

On Sep 11, 2019, at 5:18 AM, Paul Shannon notifications@github.com wrote:

Hi Tanjanay,

I am not yet able to reproduce your error here.

Could you try two things, please?

Create a tiny example script which reproduces the error. inst/sgm/wbc19-alaru.R is > 2000 lines! When you start R, type:

R> sessionInfo()

and send me the output. This tells us the version of every package you are using.

Thank you! We should be able to fix this quick.

• Paul

On Sep 10, 2019, at 6:29 PM, Paul Shannon notifications@github.com wrote:

Yes, please. So I have exactly the same code and data as you. Then tell me exactly what to do to see your error.

(Good to hear from you!)

On Sep 10, 2019, at 6:28 PM, thardy615 notifications@github.com wrote:

I did not make any changes to wbc19-aluru.R (I ran into the error after sourcing), however, I did make a new matrix for modeling so if you would like for me to push that code, I can do that. :)

Thank you!

On Tue, Sep 10, 2019 at 9:16 PM Paul Shannon < notifications@github.com> wrote:

Hi Tanjanay!

Hmmm - seems like a version error. Can you check everything into github so I can examine the problem here in Seattle? It should be a quick fix - and quite likely you have uncovered a blind spot for me to rectify. I’ll get right on it once you push your code!

• Paul

On Sep 10, 2019, at 5:14 PM, thardy615 notifications@github.com wrote:

@paul-shannon Hey Paul! I am currently building more trena models with both high and low wbc19 gene expression. I encountered this error when I tried to assign transcription factors (ex: running line 847): Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

When I ran the function MotifMatcher, it stated this in the function: else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) }

How do I prevent this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7UGOAQJG6W2UUNGEW3QJBBHRA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6M6FKI#issuecomment-530178729 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7S2RNVGGENOMHGTGMLQJBBHRANCNFSM4IVNZ6AQ

.

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7SHD6OUFIEQA2GWOVDQJDQFXA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6OKBMA#issuecomment-530358448, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7X4JQ2W7C33YYJ5LRTQJDQFXANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

Here is the output:

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3
[4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1
[7] GenomeInfoDb_1.20.0 trena_1.6.1 MotifDb_1.26.0
[10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18
[13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0
[16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0
[19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20
[22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1
[25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0
[5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4
[9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0
[13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0
[17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1
[21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0
[25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5
[29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16
[33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4
[37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1
[41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5
[45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12
[49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1
[53] flare_1.6.0.2 memoise_1.1.0

[paul-shannon]

Cool - thank you.

trena is now up to version 1.7.7 - you have 1.6.1. trena includes the MotifMatcher class - which failed on you. Maybe you installed from bioconductor? That would have been a sensible move.

Try this:

cd ~/github # or wherever you keep github packages on your computer

1) if a trena directory exists (I suspect not): cd trena; git pull

2) if no ~/github/trena directory exists: git clone https://github.com/PriceLab/trena.git cd trena

then, for both 1 & 2:

 make -f build.makefile
 make -f build.makefile test

Then - I bet you 50 cents - all will be well. We may have a bit more fussing to do. But not much

• Paul

On Sep 11, 2019, at 10:06 AM, thardy615 notifications@github.com wrote:

Here is the output:

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3 [4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1 [7] GenomeInfoDb_1.20.0 trena_1.6.1 MotifDb_1.26.0 [10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18 [13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0 [16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0 [19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20 [22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1 [25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0 [5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4 [9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0 [13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0 [17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1 [21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0 [25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5 [29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16 [33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4 [37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1 [41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5 [45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12 [49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1 [53] flare_1.6.0.2 memoise_1.1.0

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

I did exactly what you said. Here is the updated info from executing sessionInfo():

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3 [4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1 [7] GenomeInfoDb_1.20.0 trena_1.7.7 MotifDb_1.26.0 [10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18 [13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0 [16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0 [19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20 [22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1 [25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0 [5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4 [9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0 [13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0 [17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1 [21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0 [25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5 [29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16 [33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4 [37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1 [41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5 [45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12 [49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1 [53] flare_1.6.0.2 memoise_1.1.0

However I am still getting the same error after sourcing

source('~/github/TrenaProjectArabidopsisRoot/explore/networks/v1/trenaModel.1.WBC19.R') Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

On Wed, Sep 11, 2019 at 1:17 PM Paul Shannon notifications@github.com wrote:

Cool - thank you.

trena is now up to version 1.7.7 - you have 1.6.1. trena includes the MotifMatcher class - which failed on you. Maybe you installed from bioconductor? That would have been a sensible move.

Try this:

cd ~/github # or wherever you keep github packages on your computer

1) if a trena directory exists (I suspect not): cd trena; git pull

2) if no ~/github/trena directory exists: git clone https://github.com/PriceLab/trena.git cd trena

then, for both 1 & 2:

make -f build.makefile make -f build.makefile test

Then - I bet you 50 cents - all will be well. We may have a bit more fussing to do. But not much

• Paul

On Sep 11, 2019, at 10:06 AM, thardy615 notifications@github.com wrote:

Here is the output:

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3 [4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1 [7] GenomeInfoDb_1.20.0 trena_1.6.1 MotifDb_1.26.0 [10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18 [13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0 [16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0 [19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20 [22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1 [25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0 [5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4 [9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0 [13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0 [17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1 [21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0 [25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5 [29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16 [33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4 [37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1 [41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5 [45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12 [49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1 [53] flare_1.6.0.2 memoise_1.1.0

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7U62CQMMW642HXNZPDQJER2FA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PHF5A#issuecomment-530477812, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7RSKPI7VE6G7YEBHFLQJER2FANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

excellent error report! I’m on it. Response soon.

On Sep 11, 2019, at 11:20 AM, thardy615 notifications@github.com wrote:

I did exactly what you said. Here is the updated info from executing sessionInfo():

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3 [4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1 [7] GenomeInfoDb_1.20.0 trena_1.7.7 MotifDb_1.26.0 [10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18 [13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0 [16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0 [19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20 [22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1 [25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0 [5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4 [9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0 [13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0 [17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1 [21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0 [25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5 [29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16 [33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4 [37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1 [41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5 [45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12 [49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1 [53] flare_1.6.0.2 memoise_1.1.0

However I am still getting the same error after sourcing

source('~/github/TrenaProjectArabidopsisRoot/explore/networks/v1/trenaModel.1.WBC19.R') Error in MotifMatcher("tair10", as.list(pfms), quiet = TRUE) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

On Wed, Sep 11, 2019 at 1:17 PM Paul Shannon notifications@github.com wrote:

Cool - thank you.

trena is now up to version 1.7.7 - you have 1.6.1. trena includes the MotifMatcher class - which failed on you. Maybe you installed from bioconductor? That would have been a sensible move.

Try this:

cd ~/github # or wherever you keep github packages on your computer

1) if a trena directory exists (I suspect not): cd trena; git pull

2) if no ~/github/trena directory exists: git clone https://github.com/PriceLab/trena.git cd trena

then, for both 1 & 2:

make -f build.makefile make -f build.makefile test

Then - I bet you 50 cents - all will be well. We may have a bit more fussing to do. But not much

• Paul

On Sep 11, 2019, at 10:06 AM, thardy615 notifications@github.com wrote:

Here is the output:

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] org.At.tair.db_3.8.2 TrenaProjectArabidopsisRoot_1.0.8 TrenaProject_1.2.3 [4] trenaSGM_1.0.1 org.Hs.eg.db_3.8.2 GenomicRanges_1.36.1 [7] GenomeInfoDb_1.20.0 trena_1.6.1 MotifDb_1.26.0 [10] Biostrings_2.52.0 XVector_0.24.0 glmnet_2.0-18 [13] foreach_1.4.7 GO.db_3.8.2 GOstats_2.50.0 [16] Category_2.50.0 Matrix_1.2-17 GSEABase_1.46.0 [19] graph_1.62.0 annotate_1.62.0 XML_3.98-1.20 [22] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1 [25] Biobase_2.44.0 BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 Rsamtools_2.0.0 zeallot_0.1.0 [5] digest_0.6.20 lassopv_0.2.0 lars_1.2 backports_1.1.4 [9] RSQLite_2.1.2 pillar_1.4.2 zlibbioc_1.30.0 rlang_0.4.0 [13] RPostgreSQL_0.6-2 rstudioapi_0.10 data.table_1.12.2 Rgraphviz_2.28.0 [17] blob_1.2.0 splines_3.6.1 RMySQL_0.10.17 BiocParallel_1.18.1 [21] igraph_1.2.4.1 RCurl_1.95-4.12 bit_1.1-14 DelayedArray_0.10.0 [25] compiler_3.6.1 rtracklayer_1.44.4 pkgconfig_2.0.2 vbsr_0.0.5 [29] SummarizedExperiment_1.14.1 tibble_2.1.3 GenomeInfoDbData_1.2.1 codetools_0.2-16 [33] matrixStats_0.55.0 randomForest_4.6-14 AnnotationForge_1.26.0 crayon_1.3.4 [37] GenomicAlignments_1.20.1 MASS_7.3-51.4 bitops_1.0-6 grid_3.6.1 [41] RBGL_1.60.0 xtable_1.8-4 DBI_1.0.0 magrittr_1.5 [45] genefilter_1.66.0 splitstackshape_1.4.8 vctrs_0.2.0 iterators_1.0.12 [49] tools_3.6.1 bit64_0.9-7 BSgenome_1.52.0 survival_2.44-1.1 [53] flare_1.6.0.2 memoise_1.1.0

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7U62CQMMW642HXNZPDQJER2FA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PHF5A#issuecomment-530477812, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7RSKPI7VE6G7YEBHFLQJER2FANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[paul-shannon]

@thardy615 very strange. You have the right version of trena. Please try this:

cd ~/github/trena/inst/unitTests
start R
source("test_MotifMatcher.R")
test_findMatchesByChromosomalRegion.athaliana()

It works for me!

[thardy615]

:( I ran the test and I got this result:

test_findMatchesByChromosomalRegion.athaliana() [1] --- test_findMatchesByChromosomalRegion.athaliana Error in MotifMatcher(genomeName = "tair10", pfms) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

I used the traceback and it told me:

3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName))
4. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656
5. test_findMatchesByChromosomalRegion.athaliana()

However, I could not find the code from #3 in the r script...

On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon notifications@github.com wrote:

@thardy615 https://github.com/thardy615 very strange. You have the right version of trena. Please try this:

cd ~/github/trena/inst/unitTests start R source("test_MotifMatcher.R") test_findMatchesByChromosomalRegion.athaliana()

It works for me!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

try this - before it all drives you crazy :}

R> library(trena) R> MotifMatcher

You should see a bunch of lines, including:

function (genomeName, pfms, quiet = TRUE) { genomeName <- tolower(genomeName) stopifnot(is.list(pfms)) stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10"))

What do you in fact see?

• Paul

On Sep 11, 2019, at 2:57 PM, thardy615 notifications@github.com wrote:

:( I ran the test and I got this result:

test_findMatchesByChromosomalRegion.athaliana() [1] --- test_findMatchesByChromosomalRegion.athaliana Error in MotifMatcher(genomeName = "tair10", pfms) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

I used the traceback and it told me:

3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName))
4. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656
5. test_findMatchesByChromosomalRegion.athaliana()

However, I could not find the code from #3 in the r script...

On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon notifications@github.com wrote:

@thardy615 https://github.com/thardy615 very strange. You have the right version of trena. Please try this:

cd ~/github/trena/inst/unitTests start R source("test_MotifMatcher.R") test_findMatchesByChromosomalRegion.athaliana()

It works for me!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < > https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147 > >, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ > > > > > . > > > > > > > > > -- > > Tanjanay C. Hardy > > Spelman College C'2020 > > Health Science Major > > LINCS Scholar > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > -- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < > https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147 > >, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ > > > > > . > > > > > > > > > -- > > Tanjanay C. Hardy > > Spelman College C'2020 > > Health Science Major > > LINCS Scholar > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > -- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon notifications@github.com wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < > https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147 > >, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ > > > > > . > > > > > > > > > -- > > Tanjanay C. Hardy > > Spelman College C'2020 > > Health Science Major > > LINCS Scholar > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7Q3CVMN47FSSX542ZTQJFUAFA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QBRAA#issuecomment-530585728 , > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AMMDG7SRMNVUBJI5BBCPUBLQJFUAFANCNFSM4IVNZ6AQ > . > -- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[paul-shannon]

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon notifications@github.com wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < > https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147 > >, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ > > > > > . > > > > > > > > > -- > > Tanjanay C. Hardy > > Spelman College C'2020 > > Health Science Major > > LINCS Scholar > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7Q3CVMN47FSSX542ZTQJFUAFA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QBRAA#issuecomment-530585728 , > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AMMDG7SRMNVUBJI5BBCPUBLQJFUAFANCNFSM4IVNZ6AQ > . > -- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[paul-shannon]

Hi Tanjany,

If this is not working yet, let’s talk it through on the phone - get it solved!

• Paul

On Sep 11, 2019, at 3:55 PM, Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon notifications@github.com wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < > https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147 > >, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AMMDG7XIMQCDZ22YCVYT5G3QJE3MZANCNFSM4IVNZ6AQ > > > > > . > > > > > > > > > -- > > Tanjanay C. Hardy > > Spelman College C'2020 > > Health Science Major > > LINCS Scholar > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7Q3CVMN47FSSX542ZTQJFUAFA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QBRAA#issuecomment-530585728 , > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AMMDG7SRMNVUBJI5BBCPUBLQJFUAFANCNFSM4IVNZ6AQ > . > -- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[thardy615]

Hey Paul,

I got pretty busy (& honestly, pretty frustrated) so I put it to the side for a day. Is it okay if I call you tomorrow @11:30 PST?

-Tanjanay

On Thu, Sep 12, 2019 at 8:02 PM Paul Shannon notifications@github.com wrote:

Hi Tanjany,

If this is not working yet, let’s talk it through on the phone - get it solved!

• Paul

On Sep 11, 2019, at 3:55 PM, Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon <notifications@github.com

wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon < notifications@github.com> wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 < notifications@github.com> wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < >

https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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[paul-shannon]

That’s a great time to call!

• Paul

On Sep 12, 2019, at 5:23 PM, thardy615 notifications@github.com wrote:

Hey Paul,

I got pretty busy (& honestly, pretty frustrated) so I put it to the side for a day. Is it okay if I call you tomorrow @11:30 PST?

-Tanjanay

On Thu, Sep 12, 2019 at 8:02 PM Paul Shannon notifications@github.com wrote:

Hi Tanjany,

If this is not working yet, let’s talk it through on the phone - get it solved!

• Paul

On Sep 11, 2019, at 3:55 PM, Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon <notifications@github.com

wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon < notifications@github.com> wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 < notifications@github.com> wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < >

https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147

,

or mute the thread <

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

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— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ

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[thardy615]

HongQinBIO-MBP:trena bioadmin$ R CMD INSTALL. /Library/Frameworks/R.framework/Resources/bin/Rcmd: line 62: exec: INSTALL.: not found

Thank you!! :)

On Wed, Sep 11, 2019 at 6:55 PM Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon notifications@github.com wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon < notifications@github.com> wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615

wrote:

:( I ran the test and I got this result:

test_findMatchesByChromosomalRegion.athaliana() [1] --- test_findMatchesByChromosomalRegion.athaliana Error in MotifMatcher(genomeName = "tair10", pfms) : MotifMatch, genomeName not in hg19, hg38: 'tair10'

I used the traceback and it told me:

3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName))
4. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656
5. test_findMatchesByChromosomalRegion.athaliana()

However, I could not find the code from #3 in the r script...

On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> wrote:

@thardy615 https://github.com/thardy615 very strange. You have the right version of trena. Please try this:

cd ~/github/trena/inst/unitTests start R source("test_MotifMatcher.R") test_findMatchesByChromosomalRegion.athaliana()

It works for me!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147

,

or mute the thread <

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.

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7XEXMLQKSUV5U54UQDQJFZPLA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QEKKA#issuecomment-530597160, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7TBTQAMR774YS4Y2LTQJFZPLANCNFSM4IVNZ6AQ .

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[thardy615]

HongQinBIO-MBP:trena bioadmin$ R CMD install usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 file2 install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 ... fileN directory install -d [-v] [-g group] [-m mode] [-o owner] directory ...

On Fri, Sep 13, 2019 at 3:44 PM Tanjanay C Hardy thardy1@scmail.spelman.edu wrote:

HongQinBIO-MBP:trena bioadmin$ R CMD INSTALL. /Library/Frameworks/R.framework/Resources/bin/Rcmd: line 62: exec: INSTALL.: not found

Thank you!! :)

On Wed, Sep 11, 2019 at 6:55 PM Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon notifications@github.com wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon < notifications@github.com> wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 < notifications@github.com> wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < >

https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147

,

or mute the thread <

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

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,

or mute the thread <

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

[thardy615]

R -f inst/unitTests/test_MotifMatcher.R

On Fri, Sep 13, 2019 at 3:45 PM Tanjanay C Hardy thardy1@scmail.spelman.edu wrote:

HongQinBIO-MBP:trena bioadmin$ R CMD install usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 file2 install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode] [-o owner] file1 ... fileN directory install -d [-v] [-g group] [-m mode] [-o owner] directory ...

On Fri, Sep 13, 2019 at 3:44 PM Tanjanay C Hardy < thardy1@scmail.spelman.edu> wrote:

HongQinBIO-MBP:trena bioadmin$ R CMD INSTALL. /Library/Frameworks/R.framework/Resources/bin/Rcmd: line 62: exec: INSTALL.: not found

Thank you!! :)

On Wed, Sep 11, 2019 at 6:55 PM Paul Shannon notifications@github.com wrote:

very mysterious.

How many bytes for R/MotifMatcher.R?

Then do a fresh

git pull make -f build.makefile make -f build.makefile test

After you check that, try these steps, copy and paste the result for me to see (and sorry for all the fuss!):

git remote -v git branch -v

Here’s what I see:

book.trena> git branch -v

• master 8d33e66 test_MotifMatcher runTests if not interactive

book.trena> git remote -v origin git@github.com:PriceLab/trena.git (fetch) origin git@github.com:PriceLab/trena.git (push)

On Sep 11, 2019, at 3:47 PM, thardy615 notifications@github.com wrote:

the time stamp tells me today because that's when I git pulled trena. However, is there a way to see when it was created or edited? Also, test_MotifMatcher.R has 33538 bytes

On Wed, Sep 11, 2019 at 6:18 PM Paul Shannon <notifications@github.com

wrote:

You have an out of date version!

What is the time stamp on the file? How many bytes?

• Paul

On Sep 11, 2019, at 3:17 PM, thardy615 notifications@github.com wrote:

I see the following:

function (genomeName, pfms, quiet = TRUE) { stopifnot(is.list(pfms)) if (genomeName == "hg38") { reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } else if (genomeName == "hg19") { reference.genome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 } else if (genomeName == "mm10") { reference.genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 } else { stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", genomeName)) } .MotifMatcher(genome = reference.genome, pfms = pfms, quiet = quiet) } <bytecode: 0x7fcac1a53e38>

On Wed, Sep 11, 2019 at 6:09 PM Paul Shannon < notifications@github.com> wrote: > try this - before it all drives you crazy :} > > R> library(trena) > R> MotifMatcher > > You should see a bunch of lines, including: > > function (genomeName, pfms, quiet = TRUE) > { > genomeName <- tolower(genomeName) > stopifnot(is.list(pfms)) > stopifnot(genomeName %in% c("hg19", "hg38", "saccer3", "tair10")) > > What do you in fact see? > > - Paul > > > On Sep 11, 2019, at 2:57 PM, thardy615 < notifications@github.com> wrote: > > > > :( I ran the test and I got this result: > > > test_findMatchesByChromosomalRegion.athaliana() > > [1] --- test_findMatchesByChromosomalRegion.athaliana > > Error in MotifMatcher(genomeName = "tair10", pfms) : > > MotifMatch, genomeName not in hg19, hg38: 'tair10' > > > > I used the traceback and it told me: > > 3. stop(sprintf("MotifMatch, genomeName not in hg19, hg38: '%s'", > > genomeName)) > > 2. MotifMatcher(genomeName = "tair10", pfms) at test_MotifMatcher.R#656 > > 1. test_findMatchesByChromosomalRegion.athaliana() > > > > However, I could not find the code from #3 in the r script... > > > > On Wed, Sep 11, 2019 at 2:39 PM Paul Shannon < notifications@github.com> > > wrote: > > > > > @thardy615 very strange. You have the > > > right version of trena. > > > Please try this: > > > > > > cd ~/github/trena/inst/unitTests > > > start R > > > source("test_MotifMatcher.R") > > > test_findMatchesByChromosomalRegion.athaliana() > > > > > > It works for me! > > > > > > — > > > You are receiving this because you were mentioned. > > > Reply to this email directly, view it on GitHub > > > < >

https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7TO3L3RBFYJAPYNFTLQJE3MZA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PPKKY#issuecomment-530511147

,

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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,

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7VQ2EBDZ2Z6QRP4Z73QJFVDHA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QCEDY#issuecomment-530588175 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AMMDG7W4NX36YCEDHQ6ZYT3QJFVDHANCNFSM4IVNZ6AQ

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-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PriceLab/TrenaProjectArabidopsisRoot/issues/18?email_source=notifications&email_token=AMMDG7XEXMLQKSUV5U54UQDQJFZPLA5CNFSM4IVNZ6A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QEKKA#issuecomment-530597160, or mute the thread https://github.com/notifications/unsubscribe-auth/AMMDG7TBTQAMR774YS4Y2LTQJFZPLANCNFSM4IVNZ6AQ .

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar

-- Tanjanay C. Hardy Spelman College C'2020 Health Science Major LINCS Scholar