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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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Unable to build vignette #86

Closed h-joshi closed 4 years ago

h-joshi commented 4 years ago

I've tried repeatedly to build the vignette for this package with little success. These are the steps I took along with the output. Any idea why this might be happening?

Alternatively, would it be possible to also include an already built PDF copy of the vignette. The bits I am particularly interested in are the syntax nuances in using FRASER to get split and non-split counts

I'm doing this on Mac OS Sierra

Steps I took:

  1. git cloned gagneurlab/FRASER repo
  2. Installed devtools
  3. Navigated to FRASER folder

  4. R session involved & devtools::build(pkg='.', vignettes=TRUE)

    > devtools::build(pkg='.', vignettes=TRUE)
✔  checking for file ‘/Users/himanshujoshi/PycharmProjects/FRASER/DESCRIPTION’ ...
─  preparing ‘FRASER’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
E  creating vignettes (2m 19.9s)
--- re-building ‘FraseR.Rnw’ using knitr
Fri Jan 17 15:27:01 2020: Calculate the PSI 5 and 3 values ...
Fri Jan 17 15:27:03 2020: Calculate the PSI site values ...
Fri Jan 17 15:27:04 2020: Calculate the delta for psi5 values ...
Fri Jan 17 15:27:04 2020: Calculate the delta for psi3 values ...
Fri Jan 17 15:27:04 2020: Calculate the delta for psiSite values ...
Fri Jan 17 15:27:05 2020: Writing final FraseR object ('/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/savedObjects/Example_Dataset/fds-object.RDS').

Fri Jan 17 15:27:05 2020: Fit step for: 'psi5'.
Fri Jan 17 15:27:06 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:06 2020: Computing PCA ...
Fri Jan 17 15:27:06 2020: Fitting rho ...
Fri Jan 17 15:27:07 2020: Compute p values for: 'psi5'.
Fri Jan 17 15:27:08 2020: Adjust p values for: 'psi5'.
Fri Jan 17 15:27:08 2020: Compute Z scores for: 'psi5'.

Fri Jan 17 15:27:08 2020: Fit step for: 'psi3'.
Fri Jan 17 15:27:09 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:09 2020: Computing PCA ...
Fri Jan 17 15:27:09 2020: Fitting rho ...
Fri Jan 17 15:27:10 2020: Compute p values for: 'psi3'.
Fri Jan 17 15:27:11 2020: Adjust p values for: 'psi3'.
Fri Jan 17 15:27:11 2020: Compute Z scores for: 'psi3'.

Fri Jan 17 15:27:12 2020: Fit step for: 'psiSite'.
Fri Jan 17 15:27:12 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:12 2020: Computing PCA ...
Fri Jan 17 15:27:12 2020: Fitting rho ...
Fri Jan 17 15:27:13 2020: Compute p values for: 'psiSite'.
Fri Jan 17 15:27:14 2020: Adjust p values for: 'psiSite'.
Fri Jan 17 15:27:15 2020: Compute Z scores for: 'psiSite'.
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Fri Jan 17 15:27:18 2020: Collecting results for: psi5
Fri Jan 17 15:27:18 2020: Process chunk: 1 for: psi5
Fri Jan 17 15:27:18 2020: Collecting results for: psi3
Fri Jan 17 15:27:18 2020: Process chunk: 1 for: psi3
Fri Jan 17 15:27:18 2020: Collecting results for: psiSite
Fri Jan 17 15:27:18 2020: Process chunk: 1 for: psiSite
Warning in has_utility("convert", "ImageMagick") :
 ImageMagick not installed or not in PATH
Fri Jan 17 15:27:22 2020: Start counting the split reads ...
Fri Jan 17 15:27:22 2020: Count split reads for sample: sample1
Warning in dir.create(cachedir, recursive = TRUE) :
 '/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/cache/splitCounts' already exists
Fri Jan 17 15:27:22 2020: Count split reads for sample: sample2
Fri Jan 17 15:27:22 2020: Count split reads for sample: sample3
Warning in dir.create(cachedir, recursive = TRUE) :
 '/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/cache/splitCounts' already exists
Fri Jan 17 15:27:33 2020 : count ranges need to be merged ...
Fri Jan 17 15:27:35 2020: Create splice site indices ...
Fri Jan 17 15:27:35 2020: Writing counts to file: /var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/savedObjects/Data_Analysis/splitCounts.tsv.gz
Fri Jan 17 15:27:35 2020: Create splice site indices ...
Fri Jan 17 15:27:35 2020: Start counting the non spliced reads ...
Fri Jan 17 15:27:35 2020: In total 60 splice junctions are found.
Fri Jan 17 15:27:35 2020: In total 77 splice sites (acceptor/donor) will be counted ...
Fri Jan 17 15:27:35 2020: Count non spliced reads for sample: sample1
Warning in dir.create(cachedir, recursive = TRUE) :
 '/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/cache/nonSplicedCounts/Data_Analysis' already exists

       ==========     _____ _    _ ____  _____  ______          _____
       =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
         =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
           ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
             ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
       ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      Rsubread 2.0.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           o sample1.bam                                    ||
||                                                                            ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : /var/folders/gw/rccgk_r53w316ntmdmtv1hrw0001 ... ||
||                 Threads : 3                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||          Long read mode : yes                                              ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid92802 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample1.bam...                                            ||
||    WARNING: Paired-end reads were found.                                   ||
||    Total alignments : 802                                                  ||
||    Successfully assigned alignments : 188 (23.4%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

Saving splice site cache ...
Fri Jan 17 15:27:35 2020: Count non spliced reads for sample: sample3

       ==========     _____ _    _ ____  _____  ______          _____
       =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
         =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
           ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
             ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
       ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      Rsubread 2.0.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           o sample3.bam                                    ||
||                                                                            ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : /var/folders/gw/rccgk_r53w316ntmdmtv1hrw0001 ... ||
||                 Threads : 3                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||          Long read mode : yes                                              ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid92804 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample3.bam...                                            ||
||    WARNING: Paired-end reads were found.                                   ||
||    Total alignments : 3498                                                 ||
||    Successfully assigned alignments : 866 (24.8%)                          ||
||    Running time : 0.04 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

Saving splice site cache ...
Fri Jan 17 15:27:35 2020: Count non spliced reads for sample: sample2
Warning in dir.create(cachedir, recursive = TRUE) :
 '/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/cache/nonSplicedCounts/Data_Analysis' already exists

       ==========     _____ _    _ ____  _____  ______          _____
       =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
         =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
           ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
             ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
       ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      Rsubread 2.0.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           o sample2.bam                                    ||
||                                                                            ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : /var/folders/gw/rccgk_r53w316ntmdmtv1hrw0001 ... ||
||                 Threads : 3                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||          Long read mode : yes                                              ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid92803 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample2.bam...                                            ||
||    WARNING: Paired-end reads were found.                                   ||
||    Total alignments : 4397                                                 ||
||    Successfully assigned alignments : 1011 (23.0%)                         ||
||    Running time : 0.05 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

Saving splice site cache ...
Fri Jan 17 15:27:38 2020 : Fast merging of counts ...
Fri Jan 17 15:27:39 2020: Writing counts to file: /var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/savedObjects/Data_Analysis/nonSplitCounts.tsv.gz
Fri Jan 17 15:27:41 2020: Calculate the PSI 5 and 3 values ...
Fri Jan 17 15:27:42 2020: Calculate the PSI site values ...
Fri Jan 17 15:27:42 2020: Calculate the delta for psi5 values ...
Fri Jan 17 15:27:43 2020: Calculate the delta for psi3 values ...
Fri Jan 17 15:27:43 2020: Calculate the delta for psiSite values ...
Fri Jan 17 15:27:44 2020: Writing final FraseR object ('/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/sav   Fri Jan 17 15:27:44 2020: Writing final FraseR object ('/var/folders/gw/rccgk_r53w316ntmdmtv1hrw000157/T//RtmpaEz1GE/savedObjects/Data_Analysis/fds-object.RDS').
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 165 rows containing missing values (geom_bar).

Fri Jan 17 15:27:46 2020: Fit step for: 'psi5'.
Fri Jan 17 15:27:46 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:46 2020: Computing PCA ...
Fri Jan 17 15:27:46 2020: Fitting rho ...
Fri Jan 17 15:27:47 2020: Compute p values for: 'psi5'.
Fri Jan 17 15:27:48 2020: Adjust p values for: 'psi5'.
Fri Jan 17 15:27:48 2020: Compute Z scores for: 'psi5'.

Fri Jan 17 15:27:48 2020: Fit step for: 'psi3'.
Fri Jan 17 15:27:49 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:49 2020: Computing PCA ...
Fri Jan 17 15:27:49 2020: Fitting rho ...
Fri Jan 17 15:27:50 2020: Compute p values for: 'psi3'.
Fri Jan 17 15:27:51 2020: Adjust p values for: 'psi3'.
Fri Jan 17 15:27:51 2020: Compute Z scores for: 'psi3'.

Fri Jan 17 15:27:52 2020: Fit step for: 'psiSite'.
Fri Jan 17 15:27:52 2020: Running fit with correction method: PCA
Fri Jan 17 15:27:52 2020: Computing PCA ...
Fri Jan 17 15:27:52 2020: Fitting rho ...
Fri Jan 17 15:27:53 2020: Compute p values for: 'psiSite'.
Fri Jan 17 15:27:54 2020: Adjust p values for: 'psiSite'.
Fri Jan 17 15:27:55 2020: Compute Z scores for: 'psiSite'.
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Fri Jan 17 15:27:58 2020: Collecting results for: psi5
Fri Jan 17 15:27:58 2020: Process chunk: 1 for: psi5
Fri Jan 17 15:27:58 2020: Collecting results for: psiSite
Fri Jan 17 15:27:58 2020: Process chunk: 1 for: psiSite
Fri Jan 17 15:27:58 2020: Collecting results for: psi3
Fri Jan 17 15:27:58 2020: Process chunk: 1 for: psi3
Fri Jan 17 15:27:59 2020: Collecting results for: psi3
Fri Jan 17 15:28:00 2020: Process chunk: 1 for: psi3
Fri Jan 17 15:27:59 2020: Collecting results for: psiSite
Fri Jan 17 15:28:00 2020: Process chunk: 1 for: psiSite
Fri Jan 17 15:27:59 2020: Collecting results for: psi5
Fri Jan 17 15:28:00 2020: Process chunk: 1 for: psi5
Fri Jan 17 15:28:03 2020: Running fit with correction method: PCA-BB-Decoder
125
67
dPsi filter:FALSE: 121   TRUE: 2
Exclusion matrix: TRUE: 123
Fri Jan 17 15:28:12 2020: Injecting outliers: 0 / 0 (primary/secondary)
Warning in optimHyperParams(fds, type = "psi5") :
 No outliers could be injected so the hyperparameter optimization could not run. Possible reason: too few junctions in the data.
Warning in plotEncDimSearch(fds, type = "psi5") :
 no hyperparameters were estimated for psi5
Please use `optimHyperParams` to compute them.
Warning in switch(x, psi5 = c(bquote(psi[5])), psi3 = c(bquote(psi[3])),  :
 EXPR is a "factor", treated as integer.
Consider using 'switch(as.character( * ), ...)' instead.
Warning in switch(x, psi5 = c(bquote(psi[5])), psi3 = c(bquote(psi[3])),  :
 EXPR is a "factor", treated as integer.
Consider using 'switch(as.character( * ), ...)' instead.
Warning in switch(x, psi5 = c(bquote(psi[5])), psi3 = c(bquote(psi[3])),  :
 EXPR is a "factor", treated as integer.
Consider using 'switch(as.character( * ), ...)' instead.
Error: processing vignette 'FraseR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'FraseR.tex' failed.
--- failed re-building ‘FraseR.Rnw’

SUMMARY: processing the following file failed:
 ‘FraseR.Rnw’

Error: Vignette re-building failed.
Execution halted
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  :
System command error
jjyotikataria commented 4 years ago

@h-joshi Hi, any success with this?

h-joshi commented 4 years ago

@jjyotikataria Hi - The vignette is now available on Bioconductor- FRASER

h-joshi commented 4 years ago

Withdrawing / closing issue as vignette is now available on Bioconductor