ERROR during tutorial

[chesi]

Hi, I am trying the tutorial and I get this error:

*** Running IHWcorrection

Comparison against p-vals for out Comparison against p-vals for outcontrol Trained weights on the control sample Error: 'ggsave' is not an exported object from 'namespace:cowplot'

I am using R 3.6.0 and installed chicdiff with devtools.

Can you please help? Thanks! Alessandra

[mspivakov]

That's interesting, thanks for the report. Can you please post the output of sessionInfo()?

-------- Original Message -------- Subject: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4) From: Alessandra To: RegulatoryGenomicsGroup/chicdiff CC: Subscribed

Hi, I am trying the tutorial and I get this error:

*** Running IHWcorrection

Comparison against p-vals for out Comparison against p-vals for outcontrol Trained weights on the control sample Error: 'ggsave' is not an exported object from 'namespace:cowplot'

I am using R 3.6.0 and installed chicdiff with devtools.

Can you please help? Thanks! Alessandra

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[chesi]

Here it is:

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /cm/shared/apps_chop/R/3.6.0/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps_chop/R/3.6.0/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] ChicdiffData_0.2 Chicdiff_0.4 data.table_1.12.2

loaded via a namespace (and not attached): [1] Biobase_2.44.0 IHW_1.12.0
[3] bit64_0.9-7 splines_3.6.0
[5] Formula_1.2-3 assertthat_0.2.1
[7] stats4_3.6.0 latticeExtra_0.6-28
[9] blob_1.2.0 GenomeInfoDbData_1.2.1
[11] slam_0.1-45 pillar_1.4.1
[13] RSQLite_2.1.2 backports_1.1.4
[15] lattice_0.20-38 glue_1.3.1
[17] digest_0.6.19 GenomicRanges_1.36.0
[19] RColorBrewer_1.1-2 XVector_0.24.0
[21] checkmate_1.9.4 colorspace_1.4-1
[23] cowplot_1.0.0.9000 htmltools_0.3.6
[25] Matrix_1.2-17 DESeq2_1.24.0
[27] XML_3.98-1.20 pkgconfig_2.0.2
[29] genefilter_1.66.0 zlibbioc_1.30.0
[31] purrr_0.3.2 xtable_1.8-4
[33] scales_1.0.0 fdrtool_1.2.15
[35] BiocParallel_1.18.1 htmlTable_1.13.1
[37] tibble_2.1.2 annotate_1.62.0
[39] IRanges_2.18.2 ggplot2_3.2.1
[41] SummarizedExperiment_1.14.1 hexbin_1.27.3
[43] nnet_7.3-12 BiocGenerics_0.30.0
[45] lazyeval_0.2.2 survival_2.44-1.1
[47] magrittr_1.5 crayon_1.3.4
[49] memoise_1.1.0 MASS_7.3-51.4
[51] foreign_0.8-71 tools_3.6.0
[53] matrixStats_0.54.0 stringr_1.4.0
[55] S4Vectors_0.22.0 locfit_1.5-9.1
[57] munsell_0.5.0 cluster_2.0.8
[59] DelayedArray_0.10.0 AnnotationDbi_1.46.1
[61] compiler_3.6.0 GenomeInfoDb_1.20.0
[63] rlang_0.4.0 grid_3.6.0
[65] RCurl_1.95-4.12 rstudioapi_0.10
[67] Delaporte_7.0.2 htmlwidgets_1.3
[69] bitops_1.0-6 base64enc_0.1-3
[71] FMStable_0.1-2 gtable_0.3.0
[73] DBI_1.0.0 R6_2.4.0
[75] gridExtra_2.3 knitr_1.23
[77] dplyr_0.8.3 zeallot_0.1.0
[79] bit_1.1-14 Hmisc_4.2-0
[81] lpsymphony_1.12.0 stringi_1.4.3
[83] parallel_3.6.0 Chicago_1.12.0
[85] Rcpp_1.0.1 harmonicmeanp_3.0
[87] geneplotter_1.62.0 vctrs_0.2.0
[89] rpart_4.1-15 acepack_1.4.1
[91] tidyselect_0.2.5 xfun_0.7

Thanks!

[mspivakov]

Thanks! Could you run

library(cowplot)

Before running chicdiff?

Let me know if it solves the problem!

[mspivakov]

If it doesn't, let me know what happens if you run

library(ggplot2)

[chesi]

library(cowplot) doesn’t help (same error).

Can this be the problem:

library(cowplot)

---

Note: As of version 1.0.0, cowplot does not change the

default ggplot2 theme anymore. To recover the previous

behavior, execute:

theme_set(theme_cowplot())

---

From: mspivakov notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Wednesday, September 11, 2019 at 1:48 PM To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: Alessandra a.chesi@gmail.com, Author author@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4)

Thanks! Could you run

library(cowplot)

Before running chicdiff?

Let me know if it solves the problem!

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

[chesi]

library(ggplot2) didn’t help either (same error)

From: mspivakov notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Wednesday, September 11, 2019 at 1:50 PM To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: Alessandra a.chesi@gmail.com, Author author@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4)

If it doesn't, let me know what happens if you run

library(ggplot2)

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

[mspivakov]

Ok, thanks! We'll need to patch the code to fix this namespace issue then. Are you comfortable modifying the chicdiff package or shall we try things on our end and get back to you?

[chesi]

I’d prefer you do it thanks!

From: mspivakov notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Wednesday, September 11, 2019 at 2:01 PM To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: Alessandra a.chesi@gmail.com, Author author@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4)

Ok, thanks! We'll need to patch the code to fix this namespace issue then. Are you comfortable modifying the chicdiff package or shall we try things on our end and get back to you?

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[mspivakov]

Ok, then please give us a week or so to get back to you.

[chesi]

Thanks!

From: mspivakov notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Wednesday, September 11, 2019 at 3:04 PM To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: Alessandra a.chesi@gmail.com, Author author@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4)

Ok, then please give us a week or so to get back to you.

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[vmalysheva]

Hi Alessandra! Please check an updated version. Should be good now :)

[chesi]

Hi, I just installed the updated version and tried the tutorial, and I got this error:

*** Running IHWcorrection

Comparison against p-vals for out Comparison against p-vals for outcontrol Trained weights on the control sample Saving 7 x 7 in image Saving 7 x 7 in image Learned distance dependency applied to test data Error in as.environment(where) : no item called "package:cowplot" on the search list

[chesi]

This is my session info:

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /cm/shared/apps_chop/R/3.6.0/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps_chop/R/3.6.0/lib64/R/lib/libRlapack.so

locale: [1] en_US.UTF-8

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

other attached packages: [1] ChicdiffData_0.2 Chicdiff_0.5 data.table_1.12.2 devtools_2.2.0
[5] usethis_1.5.1

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.54.0
[3] fs_1.3.1 bit64_0.9-7
[5] RColorBrewer_1.1-2 rprojroot_1.3-2
[7] GenomeInfoDb_1.20.0 tools_3.6.0
[9] backports_1.1.4 R6_2.4.0
[11] DT_0.8 rpart_4.1-15
[13] DBI_1.0.0 Hmisc_4.2-0
[15] lazyeval_0.2.2 BiocGenerics_0.30.0
[17] colorspace_1.4-1 nnet_7.3-12
[19] withr_2.1.2 tidyselect_0.2.5
[21] gridExtra_2.3 prettyunits_1.0.2
[23] processx_3.3.1 DESeq2_1.24.0
[25] bit_1.1-14 curl_3.3
[27] compiler_3.6.0 fdrtool_1.2.15
[29] cli_1.1.0 Biobase_2.44.0
[31] htmlTable_1.13.1 desc_1.2.0
[33] DelayedArray_0.10.0 labeling_0.3
[35] harmonicmeanp_3.0 slam_0.1-45
[37] scales_1.0.0 checkmate_1.9.4
[39] hexbin_1.27.3 genefilter_1.66.0
[41] callr_3.2.0 Delaporte_7.0.2
[43] stringr_1.4.0 digest_0.6.19
[45] foreign_0.8-71 FMStable_0.1-2
[47] XVector_0.24.0 base64enc_0.1-3
[49] pkgconfig_2.0.2 htmltools_0.3.6
[51] Chicago_1.12.0 sessioninfo_1.1.1
[53] lpsymphony_1.12.0 htmlwidgets_1.3
[55] rlang_0.4.0 RSQLite_2.1.2
[57] rstudioapi_0.10 IHW_1.12.0
[59] BiocParallel_1.18.1 acepack_1.4.1
[61] dplyr_0.8.3 RCurl_1.95-4.12
[63] magrittr_1.5 GenomeInfoDbData_1.2.1
[65] Formula_1.2-3 Matrix_1.2-17
[67] Rcpp_1.0.1 munsell_0.5.0
[69] S4Vectors_0.22.0 stringi_1.4.3
[71] MASS_7.3-51.4 SummarizedExperiment_1.14.1 [73] zlibbioc_1.30.0 pkgbuild_1.0.5
[75] blob_1.2.0 grid_3.6.0
[77] parallel_3.6.0 crayon_1.3.4
[79] lattice_0.20-38 cowplot_1.0.0
[81] splines_3.6.0 annotate_1.62.0
[83] locfit_1.5-9.1 zeallot_0.1.0
[85] knitr_1.23 ps_1.3.0
[87] pillar_1.4.1 GenomicRanges_1.36.0
[89] geneplotter_1.62.0 stats4_3.6.0
[91] pkgload_1.0.2 XML_3.98-1.20
[93] glue_1.3.1 latticeExtra_0.6-28
[95] remotes_2.1.0 vctrs_0.2.0
[97] testthat_2.2.1 gtable_0.3.0
[99] purrr_0.3.2 assertthat_0.2.1
[101] ggplot2_3.2.1 xfun_0.7
[103] xtable_1.8-4 survival_2.44-1.1
[105] tibble_2.1.2 AnnotationDbi_1.46.1
[107] memoise_1.1.0 IRanges_2.18.2
[109] cluster_2.0.8 ellipsis_0.2.0.1

[vmalysheva]

Hi! Please try now :)

[chesi]

I think it worked this time.

The only thing is that the Rplots.pdf file it produced cannot be opened (the png files are OK).

Thanks!

From: vmalysheva notifications@github.com Reply-To: RegulatoryGenomicsGroup/chicdiff reply@reply.github.com Date: Wednesday, September 25, 2019 at 11:31 AM To: RegulatoryGenomicsGroup/chicdiff chicdiff@noreply.github.com Cc: Alessandra a.chesi@gmail.com, Author author@noreply.github.com Subject: Re: [RegulatoryGenomicsGroup/chicdiff] ERROR during tutorial (#4)

Hi! Please try now :)

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[vmalysheva]

Great! Don't worry about the Rplots.pdf, it is not important at all :) The important plots are the diffbaitPlot and the IHW control plots.