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Bioconductor / BiocCheck

http://bioconductor.org/packages/BiocCheck
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BiocCheck() dies on some packages before completing #199

Closed hpages closed 10 months ago

hpages commented 1 year ago

The packages that trigger premature exit of BiocCheck() were identified by the experimental BiocCheck automated builds. These are the packages for which the BiocCheck results are not available (NA status): BiocStyle, Biostrings, DynDoc, GenomicAlignments, rBiopaxParser, Rgraphviz, S4Vectors, and ShortRead.

Note that we only run these builds on a small subset of Bioconductor software packages at the moment, so we don't know whether or not other packages are affected.

Here's the output produced by BiocCheck() on these packages:

BiocStyle:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BiocStyle_2.29.2.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: BiocStyle
─ PackageVersion: 2.29.2
─ sourceDir: /tmp/RtmpViBvOK/file2ead2642f3e997/BiocStyle
─ installDir: /tmp/RtmpViBvOK/file2ead2620cbf367
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/BiocStyle.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* 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...
    * ERROR: Add biocViews other than Software
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * ERROR: More than one VignetteEngine specified.
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'widefig', which has been used for the chunk:
par(mar=c(4,4,0.5,0.5))
plot(cars)
---
Backtrace:
1. BiocCheck::BiocCheck("BiocStyle_2.29.2.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

Biostrings:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Biostrings_2.69.2.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: Biostrings
─ PackageVersion: 2.69.2
─ sourceDir: /tmp/RtmpLhQbiu/file2ead646eb64f74/Biostrings
─ installDir: /tmp/RtmpLhQbiu/file2ead6444abd0aa
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/Biostrings.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.0.0 to 4.3.0.
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
    * WARNING: Package files exceed the 5MB size limit.
    * WARNING: Data files exceed the 5MB size limit.
* 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:
      LongRead
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'e2', which has been used for the chunk:
v12[v12 == v12[4]]
v12[v12 == v12[1]]
---
Backtrace:
1. BiocCheck::BiocCheck("Biostrings_2.69.2.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

DynDoc:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DynDoc_1.79.0.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: DynDoc
─ PackageVersion: 1.79.0
─ sourceDir: /tmp/RtmpBuAaJi/file2ec6e64641e203/DynDoc
─ installDir: /tmp/RtmpBuAaJi/file2ec6e670902cbf
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/DynDoc.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of DynDoc...
    * WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
Warning in min(opar[opar > x]) :
  no non-missing arguments to min; returning Inf
Error in seq.default(dots[[1L]][[1L]], dots[[2L]][[1L]]) : 
  'from' must be a finite number
Calls: <Anonymous> ... .findSymbolRanges -> Map -> mapply -> <Anonymous> -> seq.default
Execution halted

GenomicAlignments:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicAlignments_1.37.0.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: GenomicAlignments
─ PackageVersion: 1.37.0
─ sourceDir: /tmp/RtmpNBzBWQ/file2ed55a109772f3/GenomicAlignments
─ installDir: /tmp/RtmpNBzBWQ/file2ed55a3752dc89
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/GenomicAlignments.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.0.0 to 4.3.0.
* 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:
      QualityControl
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'U3.OV00_Lrqseq_and_Rrqseq', which has been used for the chunk:
U3.OV00_Lrqseq <- U3.GALP_rqseq1[queryHits(U3.OV00)]
U3.OV00_Rrqseq <- U3.GALP_rqseq2[queryHits(U3.OV00)]
---
Backtrace:
1. BiocCheck::BiocCheck("GenomicAlignments_1.37.0.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

rBiopaxParser:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rBiopaxParser_2.41.0.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: rBiopaxParser
─ PackageVersion: 2.41.0
─ sourceDir: /tmp/Rtmpt7HyMc/file2f014a5bf1d534/rBiopaxParser
─ installDir: /tmp/Rtmpt7HyMc/file2f014a370562fd
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/rBiopaxParser.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.0 to 4.3.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 2)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * WARNING: Evaluate more vignette chunks.
        14 out of 23 code chunks = 60% unevaluated
        0 non-exec code chunk(s) (e.g., '```r')
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'examplereactome1', which has been used for the chunk:
file = downloadBiopaxData("reactome","reactome", version="biopax3")
---
Backtrace:
1. BiocCheck::BiocCheck("rBiopaxParser_2.41.0.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

Rgraphviz:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Rgraphviz_2.45.0.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: Rgraphviz
─ PackageVersion: 2.45.0
─ sourceDir: /tmp/RtmpIsCAmL/file2f017470c8664f/Rgraphviz
─ installDir: /tmp/RtmpIsCAmL/file2f01742b2b4a2e
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/Rgraphviz.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
    * NOTE: Update R version dependency from 2.6.0 to 4.3.0.
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'reset', which has been used for the chunk:
nodeRenderInfo(g1) <- list(fill=list(b=NULL, d=NULL))
renderGraph(g1)
---
Backtrace:
1. BiocCheck::BiocCheck("Rgraphviz_2.45.0.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

S4Vectors:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('S4Vectors_0.39.2.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: S4Vectors
─ PackageVersion: 0.39.2
─ sourceDir: /tmp/RtmpXa4NPt/file2f3e6312f3df6/S4Vectors
─ installDir: /tmp/RtmpXa4NPt/file2f3e63615546a6
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/S4Vectors.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
    Package version 0.39.2; pre-release
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.0.0 to 4.3.0.
* 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...
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'AnnotatedSNPs', which has been used for the chunk:
setClass("AnnotatedSNPs",
    contains="SNPLocations",
    slots=c(
        geneid="character"  # a character vector of length N
    )
)
---
Backtrace:
1. BiocCheck::BiocCheck("S4Vectors_0.39.2.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

ShortRead:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ShortRead_1.59.0.tar.gz')"
###
##############################################################################
##############################################################################

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: ShortRead
─ PackageVersion: 1.59.0
─ sourceDir: /tmp/RtmptWLr3o/file2f427c405a30cf/ShortRead
─ installDir: /tmp/RtmptWLr3o/file2f427c3f5e90d3
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/ShortRead.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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:
      Coverage, Alignment, RNASeq, ImmunoOncology
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import grDevices, stats, utils in DESCRIPTION as well as
      NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Error: 
! in callr subprocess.
Caused by error in `parse_block(g[-1], g[1], params.src, markdown_mode)`:
! Duplicate chunk label 'qa-files', which has been used for the chunk:
fls <- dir("/path/to", "*fastq$", full=TRUE)
---
Backtrace:
1. BiocCheck::BiocCheck("ShortRead_1.59.0.tar.gz")
2. BiocCheck:::BiocCheckRun(package = package, checkDir = checkDir, debug = debug, …
3. BiocCheck:::checkVignetteDir(package_dir, checkingDir)
4. BiocCheck:::checkVigBiocInst(pkgdir)
5. BiocCheck:::findSymbolsInVignettes(pkgdir, Symbols = .OLD_INSTALL_CALLS, …
6. BiocCheck:::quiet_knitr_purl(input = vfile, output = tempR, quiet = TRUE)
7. callr::r(function(...) suppressWarnings(knitr::purl(...)), args = args, …
8. callr:::get_result(output = out, options)
9. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. base::suppressWarnings(knitr::purl(...))
 2. base::withCallingHandlers(expr, warning = function(w) if (inherits(w, …
 3. knitr::purl(...)
 4. knitr::knit(..., tangle = TRUE)
 5. knitr:::process_file(text, output)
 6. knitr:::split_file(lines = text)
 7. base::lapply(groups, function(g) { …
 8. local FUN(X[[i]], ...)
 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode)
10. base::stop("Duplicate chunk label '", label, "', which has been used for the chu…
11. | base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted

So all of them (except DynDoc) break BiocCheck() because of a duplicated chunk label problem, which is definitely something packages should not do, but that should not break BiocCheck() either. Ideally BiocCheck() should catch this problem and report it.

LiNk-NY commented 10 months ago

This has been resolved for packages with duplicate chunk labels. That excludes DynDoc and should be a separate issue. My impression is that DynDoc is an old package and should be deprecated / archived.

hpages commented 10 months ago

Thanks Marcel.

That excludes DynDoc and should be a separate issue. My impression is that DynDoc is an old package and should be deprecated / archived.

Maybe, but it could be argued that BiocCheck() should never die prematurly and that it's a bug in BiocCheck() if it does.

Anyways, I share the same impression as you about DynDoc but I have no idea what it does or what a good replacement would be. In the meantime I'll see if I can remove it from the experimental BiocCheck automated builds.

Thanks again, H.