machv2 Summary
[top]
| Package: surf |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data surf |
| BuildTime: 0 minutes 46.38 seconds |
| CheckCommand: BiocCheckGitClone('surf') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch surf_0.99.1.tar.gz && BiocCheck('surf_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 9.43 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh surf_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 29.56 seconds |
| PackageFileSize: 4218.05 KiB |
| BuildID:: surf_20210507174404 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: surf. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
machv2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘surf/DESCRIPTION’ ... OK
* preparing ‘surf’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘surf_0.99.1.tar.gz’
machv2 CHECK output
[top]
===============================
BiocCheckGitClone('surf')
===============================
This is BiocCheckGitClone version 1.27.16. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
surf.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck’
* using R version 4.1.0 alpha (2021-04-29 r80247)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘surf/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘surf’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘surf’ can be installed ... [29s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'drseq.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
Missing link or links in documentation object 'drseqCount.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
Missing link or links in documentation object 'import.Rd':
‘[rtracklayer:export]{rtracklayer::import}’
Missing link or links in documentation object 'prepDrseqAnno.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[9s/9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck/00check.log’
for details.
===============================
BiocCheck('surf_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.16. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Registered S3 methods overwritten by 'car':
method from
influence.merMod lme4
cooks.distance.influence.merMod lme4
dfbeta.influence.merMod lme4
dfbetas.influence.merMod lme4
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, ImmunoOncology, DifferentialExpression,
DifferentialSplicing
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of surf...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
estimate.R (line 1045, column 15)
estimate.R (line 1065, column 21)
estimate.R (line 1353, column 26)
prepare.R (line 198, column 18)
prepare.R (line 261, column 9)
prepare.R (line 338, column 24)
prepare.R (line 340, column 41)
prepare.R (line 345, column 15)
prepare.R (line 366, column 31)
prepare.R (line 401, column 16)
prepare.R (line 403, column 28)
prepare.R (line 440, column 36)
prepare.R (line 444, column 21)
prepare.R (line 463, column 26)
prepare.R (line 539, column 12)
prepare.R (line 540, column 36)
prepare.R (line 823, column 31)
* NOTE: Avoid the use of 'paste' in condition signalers
Found in files:
/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//Rtmpy2hpNC/file70a0307716c5/surf/R/prepare.R
(line 167, column 15)
* NOTE: Avoid redundancy in signalers
Found in files:
/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//Rtmpy2hpNC/file70a0307716c5/surf/R/prepare.R
(line 347, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths....
* NOTE: Recommended function length <= 50 lines.
There are 18 functions > 50 lines.
The longest 5 functions are:
featureCounts() (R/help.R, line 956): 298 lines
faseqCount() (R/estimate.R, line 608): 151 lines
getFeature() (R/prepare.R, line 732): 137 lines
annotateEvent() (R/prepare.R, line 385): 132 lines
daseq() (R/estimate.R, line 1268): 126 lines
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
daseq.Rd, daseqResults.Rd, drseq.Rd, drseqCount.Rd,
drseqFilter.Rd, drseqFit.Rd, drseqResults.Rd, fa.plot.Rd, faseq.Rd,
faseqCount.Rd, faseqFit.Rd, faseqInfer.Rd, faseqResults.Rd,
genePartsList.Rd, getAUC.Rd, getIsoPartsList.Rd, getRankings.Rd,
heatmapAUC.Rd, inferredFeature.Rd, parseEvent.Rd, plotDispFunc.Rd,
prepDrseqAnno.Rd, sampleData.Rd, volcano.plot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 177 lines (3%) are > 80 characters
long.
First 6 lines:
R/estimate.R:10 #' need the GTF input. This function helps to produce t...
R/estimate.R:23 #' @return `NULL`, the function is a procedure and only...
R/estimate.R:83 gr1 = unlist(GRangesList(S4Vectors::split(unname(gr1)...
R/estimate.R:109 # event$exonic_part_id = paste(event$gene_id, event$...
R/estimate.R:128 #' This function creates the `drseqData` slot needed b...
R/estimate.R:132 #' If annotation files are missing, this function can ...
* NOTE: Consider multiples of 4 spaces for line indents, 1625
lines(28%) are not.
First 6 lines:
R/estimate.R:27 anno.prefix = "annotation.drseq",
R/estimate.R:28 anno.format = "gff2",
R/estimate.R:29 remove.overlap.exon = FALSE,
R/estimate.R:30 cores = max(1, detectCores()-2),
R/estimate.R:31 verbose = TRUE) {
R/estimate.R:32 ## reconstruct genome annotation from @genePartsList
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* ERROR: Package must be removed from CRAN.
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 4
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
machv2 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir surf_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘surf’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (surf)
malbec2 Summary
[top]
| Package: surf |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data surf |
| BuildTime: 0 minutes 39.30 seconds |
| CheckCommand: BiocCheckGitClone('surf') && /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --no-vignettes --timings surf_0.99.1.tar.gz && BiocCheck('surf_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 4.51 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4220.06 KiB |
| BuildID:: surf_20210507174404 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: surf. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
malbec2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘surf/DESCRIPTION’ ... OK
* preparing ‘surf’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘surf_0.99.1.tar.gz’
malbec2 CHECK output
[top]
===============================
BiocCheckGitClone('surf')
===============================
This is BiocCheckGitClone version 1.27.16. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
surf.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck’
* using R version 4.1.0 alpha (2021-05-01 r80254)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘surf/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘surf’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘surf’ can be installed ... [25s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s/25s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'drseq.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
Missing link or links in documentation object 'drseqCount.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
Missing link or links in documentation object 'import.Rd':
‘[rtracklayer:export]{rtracklayer::import}’
Missing link or links in documentation object 'prepDrseqAnno.Rd':
‘[rtracklayer:export]{rtracklayer::export}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck/00check.log’
for details.
===============================
BiocCheck('surf_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.16. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Registered S3 methods overwritten by 'car':
method from
influence.merMod lme4
cooks.distance.influence.merMod lme4
dfbeta.influence.merMod lme4
dfbetas.influence.merMod lme4
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, ImmunoOncology, DifferentialExpression,
DifferentialSplicing
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of surf...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
estimate.R (line 1045, column 15)
estimate.R (line 1065, column 21)
estimate.R (line 1353, column 26)
prepare.R (line 198, column 18)
prepare.R (line 261, column 9)
prepare.R (line 338, column 24)
prepare.R (line 340, column 41)
prepare.R (line 345, column 15)
prepare.R (line 366, column 31)
prepare.R (line 401, column 16)
prepare.R (line 403, column 28)
prepare.R (line 440, column 36)
prepare.R (line 444, column 21)
prepare.R (line 463, column 26)
prepare.R (line 539, column 12)
prepare.R (line 540, column 36)
prepare.R (line 823, column 31)
* NOTE: Avoid the use of 'paste' in condition signalers
Found in files:
/tmp/RtmpTzb7D2/fileac8952e1ba4e/surf/R/prepare.R (line 167,
column 15)
* NOTE: Avoid redundancy in signalers
Found in files:
/tmp/RtmpTzb7D2/fileac8952e1ba4e/surf/R/prepare.R (line 347,
column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths....
* NOTE: Recommended function length <= 50 lines.
There are 18 functions > 50 lines.
The longest 5 functions are:
featureCounts() (R/help.R, line 956): 298 lines
faseqCount() (R/estimate.R, line 608): 151 lines
getFeature() (R/prepare.R, line 732): 137 lines
annotateEvent() (R/prepare.R, line 385): 132 lines
daseq() (R/estimate.R, line 1268): 126 lines
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
daseq.Rd, daseqResults.Rd, drseq.Rd, drseqCount.Rd,
drseqFilter.Rd, drseqFit.Rd, drseqResults.Rd, fa.plot.Rd, faseq.Rd,
faseqCount.Rd, faseqFit.Rd, faseqInfer.Rd, faseqResults.Rd,
genePartsList.Rd, getAUC.Rd, getIsoPartsList.Rd, getRankings.Rd,
heatmapAUC.Rd, inferredFeature.Rd, parseEvent.Rd, plotDispFunc.Rd,
prepDrseqAnno.Rd, sampleData.Rd, volcano.plot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 177 lines (3%) are > 80 characters
long.
First 6 lines:
R/estimate.R:10 #' need the GTF input. This function helps to produce t...
R/estimate.R:23 #' @return `NULL`, the function is a procedure and only...
R/estimate.R:83 gr1 = unlist(GRangesList(S4Vectors::split(unname(gr1)...
R/estimate.R:109 # event$exonic_part_id = paste(event$gene_id, event$...
R/estimate.R:128 #' This function creates the `drseqData` slot needed b...
R/estimate.R:132 #' If annotation files are missing, this function can ...
* NOTE: Consider multiples of 4 spaces for line indents, 1625
lines(28%) are not.
First 6 lines:
R/estimate.R:27 anno.prefix = "annotation.drseq",
R/estimate.R:28 anno.format = "gff2",
R/estimate.R:29 remove.overlap.exon = FALSE,
R/estimate.R:30 cores = max(1, detectCores()-2),
R/estimate.R:31 verbose = TRUE) {
R/estimate.R:32 ## reconstruct genome annotation from @genePartsList
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* ERROR: Package must be removed from CRAN.
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 4
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
malbec2 BUILD BIN output
[top]
tokay2 Summary
[top]
| Package: surf |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD build --keep-empty-dirs --no-resave-data surf |
| BuildTime: 0 minutes 59.14 seconds |
| CheckCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=surf.buildbin-libdir surf_0.99.1.tar.gz >surf-install.out 2>&1 && C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD check --library=surf.buildbin-libdir --install="check:surf-install.out" --force-multiarch --no-vignettes --timings surf_0.99.1.tar.gz && BiocCheck('surf_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 48.37 seconds |
| BuildBinCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=surf.buildbin-libdir surf_0.99.1.tar.gz |
| BuildBinTime: 0 minutes 44.72 seconds |
| PackageFileSize: 4157.69 KiB |
| BuildID:: surf_20210507174404 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: surf. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
tokay2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file 'surf/DESCRIPTION' ... OK
* preparing 'surf':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION
* building 'surf_0.99.1.tar.gz'
tokay2 CHECK output
[top]
Installing package prior to check...
===============================
BiocCheckGitClone('surf')
===============================
This is BiocCheckGitClone version 1.27.16. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
surf.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory 'C:/Users/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck'
* using R Under development (unstable) (2021-04-06 r80146)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'surf/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'surf' version '0.99.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'surf' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [31s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'drseq.Rd':
'[rtracklayer:export]{rtracklayer::export}'
Missing link or links in documentation object 'drseqCount.Rd':
'[rtracklayer:export]{rtracklayer::export}'
Missing link or links in documentation object 'import.Rd':
'[rtracklayer:export]{rtracklayer::import}'
Missing link or links in documentation object 'prepDrseqAnno.Rd':
'[rtracklayer:export]{rtracklayer::export}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [8s]
[9s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [8s]
[9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
'C:/Users/pkgbuild/packagebuilder/workers/jobs/2040/b8752c21c0765295132ce658785432d65689d599/surf.Rcheck/00check.log'
for details.
===============================
BiocCheck('surf_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.16. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Registered S3 methods overwritten by 'car':
method from
influence.merMod lme4
cooks.distance.influence.merMod lme4
dfbeta.influence.merMod lme4
dfbetas.influence.merMod lme4
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, ImmunoOncology, DifferentialExpression,
DifferentialSplicing
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of surf...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
estimate.R (line 1045, column 15)
estimate.R (line 1065, column 21)
estimate.R (line 1353, column 26)
prepare.R (line 198, column 18)
prepare.R (line 261, column 9)
prepare.R (line 338, column 24)
prepare.R (line 340, column 41)
prepare.R (line 345, column 15)
prepare.R (line 366, column 31)
prepare.R (line 401, column 16)
prepare.R (line 403, column 28)
prepare.R (line 440, column 36)
prepare.R (line 444, column 21)
prepare.R (line 463, column 26)
prepare.R (line 539, column 12)
prepare.R (line 540, column 36)
prepare.R (line 823, column 31)
* NOTE: Avoid the use of 'paste' in condition signalers
Found in files:
C:\Users\pkgbuild\AppData\Local\Temp\RtmpY9yTQd\fileeb024fff2/surf/R/prepare.R
(line 167, column 15)
* NOTE: Avoid redundancy in signalers
Found in files:
C:\Users\pkgbuild\AppData\Local\Temp\RtmpY9yTQd\fileeb024fff2/surf/R/prepare.R
(line 347, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths....
* NOTE: Recommended function length <= 50 lines.
There are 18 functions > 50 lines.
The longest 5 functions are:
featureCounts() (R/help.R, line 956): 298 lines
faseqCount() (R/estimate.R, line 608): 151 lines
getFeature() (R/prepare.R, line 732): 137 lines
annotateEvent() (R/prepare.R, line 385): 132 lines
daseq() (R/estimate.R, line 1268): 126 lines
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
daseq.Rd, daseqResults.Rd, drseq.Rd, drseqCount.Rd,
drseqFilter.Rd, drseqFit.Rd, drseqResults.Rd, fa.plot.Rd, faseq.Rd,
faseqCount.Rd, faseqFit.Rd, faseqInfer.Rd, faseqResults.Rd,
genePartsList.Rd, getAUC.Rd, getIsoPartsList.Rd, getRankings.Rd,
heatmapAUC.Rd, inferredFeature.Rd, parseEvent.Rd, plotDispFunc.Rd,
prepDrseqAnno.Rd, sampleData.Rd, volcano.plot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 177 lines (3%) are > 80 characters
long.
First 6 lines:
R/estimate.R:10 #' need the GTF input. This function helps to produce t...
R/estimate.R:23 #' @return `NULL`, the function is a procedure and only...
R/estimate.R:83 gr1 = unlist(GRangesList(S4Vectors::split(unname(gr1)...
R/estimate.R:109 # event$exonic_part_id = paste(event$gene_id, event$...
R/estimate.R:128 #' This function creates the `drseqData` slot needed b...
R/estimate.R:132 #' If annotation files are missing, this function can ...
* NOTE: Consider multiples of 4 spaces for line indents, 1625
lines(28%) are not.
First 6 lines:
R/estimate.R:27 anno.prefix = "annotation.drseq",
R/estimate.R:28 anno.format = "gff2",
R/estimate.R:29 remove.overlap.exon = FALSE,
R/estimate.R:30 cores = max(1, detectCores()-2),
R/estimate.R:31 verbose = TRUE) {
R/estimate.R:32 ## reconstruct genome annotation from @genePartsList
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* ERROR: Package must be removed from CRAN.
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 4
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
tokay2 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
install for i386
* installing *source* package 'surf' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'surf'
finding HTML links ... done
abs.max html
REDIRECT:topic abs.max -> abs.max.html [ SUCCESS ]
addGeneTx html
REDIRECT:topic addGeneTx -> addGeneTx.html [ SUCCESS ]
aggregateAUCbyCondition html
REDIRECT:topic aggregateAUCbyCondition -> aggregateAUCbyCondition.html [ SUCCESS ]
annotateEvent html
REDIRECT:topic annotateEvent -> annotateEvent.html [ SUCCESS ]
c_granges html
REDIRECT:topic c_granges -> c_granges.html [ SUCCESS ]
calculateAUC html
REDIRECT:topic calculateAUC -> calculateAUC.html [ SUCCESS ]
clusterByGroup html
REDIRECT:topic clusterByGroup -> clusterByGroup.html [ SUCCESS ]
countLogicRle html
REDIRECT:topic countLogicRle -> countLogicRle.html [ SUCCESS ]
daseq html
REDIRECT:topic daseq -> daseq.html [ SUCCESS ]
daseqResults-class html
REDIRECT:topic daseqResults-class -> daseqResults-class.html [ SUCCESS ]
daseqResults html
REDIRECT:topic daseqResults -> daseqResults.html [ SUCCESS ]
diffAUC html
REDIRECT:topic diffAUC -> diffAUC.html [ SUCCESS ]
drseq html
REDIRECT:topic drseq -> drseq.html [ SUCCESS ]
drseqCount html
REDIRECT:topic drseqCount -> drseqCount.html [ SUCCESS ]
drseqFilter html
REDIRECT:topic drseqFilter -> drseqFilter.html [ SUCCESS ]
drseqFit html
REDIRECT:topic drseqFit -> drseqFit.html [ SUCCESS ]
drseqResults-class html
REDIRECT:topic drseqResults-class -> drseqResults-class.html [ SUCCESS ]
drseqResults html
REDIRECT:topic drseqResults -> drseqResults.html [ SUCCESS ]
fa.plot html
REDIRECT:topic fa.plot -> fa.plot.html [ SUCCESS ]
faseq html
REDIRECT:topic faseq -> faseq.html [ SUCCESS ]
faseqCount html
REDIRECT:topic faseqCount -> faseqCount.html [ SUCCESS ]
faseqFit html
REDIRECT:topic faseqFit -> faseqFit.html [ SUCCESS ]
faseqInfer html
REDIRECT:topic faseqInfer -> faseqInfer.html [ SUCCESS ]
faseqResults-class html
REDIRECT:topic faseqResults-class -> faseqResults-class.html [ SUCCESS ]
faseqResults html
REDIRECT:topic faseqResults -> faseqResults.html [ SUCCESS ]
fat html
REDIRECT:topic fat -> fat.html [ SUCCESS ]
featureCounts html
REDIRECT:topic featureCounts -> featureCounts.html [ SUCCESS ]
findAdjacentFeature html
REDIRECT:topic findAdjacentFeature -> findAdjacentFeature.html [ SUCCESS ]
findBodyFeature html
REDIRECT:topic findBodyFeature -> findBodyFeature.html [ SUCCESS ]
findNeighborFeature html
REDIRECT:topic findNeighborFeature -> findNeighborFeature.html [ SUCCESS ]
genePartsList html
REDIRECT:topic genePartsList -> genePartsList.html [ SUCCESS ]
getASName html
REDIRECT:topic getASName -> getASName.html [ SUCCESS ]
getAUC html
REDIRECT:topic getAUC -> getAUC.html [ SUCCESS ]
REDIRECT:topic getAUC,SummarizedExperiment-method -> getAUC.html [ SUCCESS ]
REDIRECT:topic getAUC,daseqResults-method -> getAUC.html [ SUCCESS ]
REDIRECT:topic getAUC,surf-method -> getAUC.html [ SUCCESS ]
getControlSet html
REDIRECT:topic getControlSet -> getControlSet.html [ SUCCESS ]
getEES html
REDIRECT:topic getEES -> getEES.html [ SUCCESS ]
getESS html
REDIRECT:topic getESS -> getESS.html [ SUCCESS ]
getEvent html
REDIRECT:topic getEvent -> getEvent.html [ SUCCESS ]
getFeature html
REDIRECT:topic getFeature -> getFeature.html [ SUCCESS ]
getIsoAS html
REDIRECT:topic getIsoAS -> getIsoAS.html [ SUCCESS ]
getIsoPartsList html
REDIRECT:topic getIsoPartsList -> getIsoPartsList.html [ SUCCESS ]
getMultiTxGene html
REDIRECT:topic getMultiTxGene -> getMultiTxGene.html [ SUCCESS ]
getRankings html
REDIRECT:topic getRankings -> getRankings.html [ SUCCESS ]
finding level-2 HTML links ... done
getTargetSet html
REDIRECT:topic getTargetSet -> getTargetSet.html [ SUCCESS ]
heatmapAUC html
REDIRECT:topic heatmapAUC -> heatmapAUC.html [ SUCCESS ]
REDIRECT:topic heatmapAUC,SummarizedExperiment-method -> heatmapAUC.html [ SUCCESS ]
REDIRECT:topic heatmapAUC,daseqResults-method -> heatmapAUC.html [ SUCCESS ]
import html
REDIRECT:topic import -> import.html [ SUCCESS ]
inferredFeature html
REDIRECT:topic inferredFeature -> inferredFeature.html [ SUCCESS ]
list_rbind html
REDIRECT:topic list_rbind -> list_rbind.html [ SUCCESS ]
numberAS html
REDIRECT:topic numberAS -> numberAS.html [ SUCCESS ]
parseEvent html
REDIRECT:topic parseEvent -> parseEvent.html [ SUCCESS ]
plotDispFunc html
REDIRECT:topic plotDispFunc -> plotDispFunc.html [ SUCCESS ]
REDIRECT:topic plotDispFunc,drseqResults-method -> plotDispFunc.html [ SUCCESS ]
REDIRECT:topic plotDispFunc,surf-method -> plotDispFunc.html [ SUCCESS ]
prepDrseqAnno html
REDIRECT:topic prepDrseqAnno -> prepDrseqAnno.html [ SUCCESS ]
sampleData html
REDIRECT:topic sampleData -> sampleData.html [ SUCCESS ]
REDIRECT:topic sampleData,SummarizedExperiment-method -> sampleData.html [ SUCCESS ]
REDIRECT:topic sampleData,daseqResults-method -> sampleData.html [ SUCCESS ]
REDIRECT:topic sampleData,surf-method -> sampleData.html [ SUCCESS ]
stream html
REDIRECT:topic stream -> stream.html [ SUCCESS ]
surf-class html
REDIRECT:topic surf-class -> surf-class.html [ SUCCESS ]
REDIRECT:topic genePartsList,surf-method -> surf-class.html [ SUCCESS ]
REDIRECT:topic drseqResults,surf-method -> surf-class.html [ SUCCESS ]
REDIRECT:topic faseqResults,surf-method -> surf-class.html [ SUCCESS ]
REDIRECT:topic daseqResults,surf-method -> surf-class.html [ SUCCESS ]
volcano.plot html
REDIRECT:topic volcano.plot -> volcano.plot.html [ SUCCESS ]
REDIRECT:topic volcano.plot,drseqResults-method -> volcano.plot.html [ SUCCESS ]
REDIRECT:topic volcano.plot,surf-method -> volcano.plot.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'surf' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'surf' as surf_0.99.1.zip
* DONE (surf)