Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/mnmer

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)/x86_64	WARNINGS	ERROR	skipped	OK
merida1	macOS 10.14.6 Mojave/x86_64	WARNINGS	ERROR	OK	OK

nebbiolo1 Summary

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Package: mnmer

Version: 0.99.1

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mnmer

BuildTime: 0 minutes 20.08 seconds

CheckCommand: BiocCheckGitClone('mnmer') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2843/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.install-out.txt mnmer_0.99.1.tar.gz && BiocCheck('mnmer_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 1 minutes 6.97 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 1539.15 KiB

BuildID:: mnmer_20221221123818

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mnmer. 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.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘mnmer/DESCRIPTION’ ... OK
* preparing ‘mnmer’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
    ‘vignette.Rmd’, ‘vignette.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mnmer_0.99.1.tar.gz’

nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('mnmer')

===============================

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: mnmer
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
    * ERROR: Remove 'inst/doc' folder from the package source
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mnmer/DESCRIPTION’ ... OK
* this is package ‘mnmer’ 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 ‘mnmer’ 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 ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [9s/9s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘mnmer/libs/mnmer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘vignette’: ‘vignette.html’ (862824 bytes), ‘vignette.pdf’ (464788 bytes)
Package vignette without corresponding single PDF/HTML:
  ‘vignette.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.Rcheck/00check.log’
for details.






===============================

 BiocCheck('mnmer_0.99.1.tar.gz')

===============================

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: mnmer
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpE8PzaJ/file2f114c5acb782b/mnmer
─ installDir: /tmp/RtmpE8PzaJ/file2f114c50687686
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.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 new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.2.0 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:
      Sequencing, Alignment, SequenceMatching, DataImport
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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mnmer...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 41 lines (14%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 11 lines
      (4%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES

See the mnmer.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: mnmer

Version: 0.99.1

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mnmer

BuildTime: 0 minutes 53.61 seconds

CheckCommand: BiocCheckGitClone('mnmer') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2843/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.install-out.txt mnmer_0.99.1.tar.gz && BiocCheck('mnmer_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 3 minutes 4.16 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh mnmer_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 26.71 seconds

PackageFileSize: 1534.13 KiB

BuildID:: mnmer_20221221123818

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mnmer. Starting Build package. Starting Check package. Starting Build package.

merida1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘mnmer/DESCRIPTION’ ... OK
* preparing ‘mnmer’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
    ‘vignette.Rmd’, ‘vignette.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mnmer_0.99.1.tar.gz’

merida1 CHECK output

[top]

===============================

 BiocCheckGitClone('mnmer')

===============================

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: mnmer
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
    * ERROR: Remove 'inst/doc' folder from the package source
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mnmer/DESCRIPTION’ ... OK
* this is package ‘mnmer’ 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 ‘mnmer’ 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 ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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 ... [6s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/7s] OK
* checking whether the package can be unloaded cleanly ... [6s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/7s] OK
* checking loading without being on the library search path ... [6s/7s] 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 ... [21s/24s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘mnmer/libs/mnmer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [7s/8s]
 [8s/9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘vignette’: ‘vignette.html’ (854301 bytes), ‘vignette.pdf’ (464788 bytes)
Package vignette without corresponding single PDF/HTML:
  ‘vignette.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [9s/9s] OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.Rcheck/00check.log’
for details.






===============================

 BiocCheck('mnmer_0.99.1.tar.gz')

===============================

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: mnmer
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpvSVyck/filed44a3166d05/mnmer
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpvSVyck/filed44a6f65bc3f
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/mnmer.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 new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.2.0 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:
      Sequencing, Alignment, SequenceMatching, DataImport
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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mnmer...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 41 lines (14%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 11 lines
      (4%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES

See the mnmer.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

merida1 BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir mnmer_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘mnmer’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c mnmercpp.cc -o mnmercpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mnmer.so mnmercpp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2843/116fa0c10bb9c25df049c15d4f9f23cd867e56a1/libdir/00LOCK-mnmer/00new/mnmer/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mnmer)


>>>>>>> 
>>>>>>> FIXING LINKS FOR libdir/mnmer/libs/mnmer.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "libdir/mnmer/libs/mnmer.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "libdir/mnmer/libs/mnmer.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "libdir/mnmer/libs/mnmer.so"