nebbiolo1 Summary
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Package: cellxgenedp |
Version: 0.99.5 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cellxgenedp |
BuildTime: 0 minutes 30.18 seconds |
CheckCommand: BiocCheckGitClone('cellxgenedp') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings cellxgenedp_0.99.5.tar.gz && BiocCheck('cellxgenedp_0.99.5.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 45.98 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 398.73 KiB |
BuildID:: cellxgenedp_20220225174601 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: cellxgenedp. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘cellxgenedp/DESCRIPTION’ ... OK
* preparing ‘cellxgenedp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘cellxgenedp_0.99.5.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('cellxgenedp')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2522/bc6926da2349e187eb51661d59cbf92ca3118ea9/cellxgenedp.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellxgenedp/DESCRIPTION’ ... OK
* this is package ‘cellxgenedp’ version ‘0.99.5’
* 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 serialization versions ... OK
* checking whether package ‘cellxgenedp’ can be installed ... [19s/19s] 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 ... [3s/3s] 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* 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’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('cellxgenedp_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2522/bc6926da2349e187eb51661d59cbf92ca3118ea9/cellxgenedp_0.99.5.tar.gz" "/tmp/RtmphO2iIx/file72e94d68314b/lib" 2>/dev/null' had status 1
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cellxgenedp...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/db.R (line 87, column 26)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
<<- in R/db.R (line 37, column 15)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
.keys_query() (R/keys.R, line 29): 54 lines
.cellxgene_cache_get() (R/cellxgene.R, line 60): 34 lines
.cellxgene_cache_annotate() (R/cellxgene.R, line 35): 24 lines
db() (R/db.R, line 73): 23 lines
.facet() (R/facets.R, line 15): 22 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
25% of man pages use one of these cases.
Found in the following files:
query.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
query.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; 1 lines (0%) are > 80 characters
long.
First 1 lines:
vignettes/using_cellxgenedp.Rmd:17 %\VignetteIndexEntry{Discover an...
* NOTE: Consider multiples of 4 spaces for line indents, 4
lines(0%) are not.
First 4 lines:
R/cpp11.R:4 .Call(`_cellxgenedp_cpp_version`)
R/cpp11.R:8 .Call(`_cellxgenedp_cpp_jmespath`, data, path)
vignettes/using_cellxgenedp.Rmd:5 affiliation: Roswell Park Comprehen...
vignettes/using_cellxgenedp.Rmd:6 email: Martin.Morgan@RoswellPark.org
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...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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merida1 Summary
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Package: cellxgenedp |
Version: 0.99.5 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellxgenedp |
BuildTime: 0 minutes 39.82 seconds |
CheckCommand: BiocCheckGitClone('cellxgenedp') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellxgenedp_0.99.5.tar.gz && BiocCheck('cellxgenedp_0.99.5.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 56.56 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh cellxgenedp_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 19.46 seconds |
PackageFileSize: 398.69 KiB |
BuildID:: cellxgenedp_20220225174601 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: cellxgenedp. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘cellxgenedp/DESCRIPTION’ ... OK
* preparing ‘cellxgenedp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘cellxgenedp_0.99.5.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('cellxgenedp')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2522/bc6926da2349e187eb51661d59cbf92ca3118ea9/cellxgenedp.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellxgenedp/DESCRIPTION’ ... OK
* this is package ‘cellxgenedp’ version ‘0.99.5’
* 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 serialization versions ... OK
* checking whether package ‘cellxgenedp’ can be installed ... [19s/19s] 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 ... [4s/4s] 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[5s/4s] 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: OK
===============================
BiocCheck('cellxgenedp_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2522/bc6926da2349e187eb51661d59cbf92ca3118ea9/cellxgenedp_0.99.5.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpiZoiT0/file1417460abffa8/lib" 2>/dev/null' had status 1
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cellxgenedp...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/db.R (line 87, column 26)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
<<- in R/db.R (line 37, column 15)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
.keys_query() (R/keys.R, line 29): 54 lines
.cellxgene_cache_get() (R/cellxgene.R, line 60): 34 lines
.cellxgene_cache_annotate() (R/cellxgene.R, line 35): 24 lines
db() (R/db.R, line 73): 23 lines
.facet() (R/facets.R, line 15): 22 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
25% of man pages use one of these cases.
Found in the following files:
query.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
query.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; 1 lines (0%) are > 80 characters
long.
First 1 lines:
vignettes/using_cellxgenedp.Rmd:17 %\VignetteIndexEntry{Discover an...
* NOTE: Consider multiples of 4 spaces for line indents, 4
lines(0%) are not.
First 4 lines:
R/cpp11.R:4 .Call(`_cellxgenedp_cpp_version`)
R/cpp11.R:8 .Call(`_cellxgenedp_cpp_jmespath`, data, path)
vignettes/using_cellxgenedp.Rmd:5 affiliation: Roswell Park Comprehen...
vignettes/using_cellxgenedp.Rmd:6 email: Martin.Morgan@RoswellPark.org
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...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir cellxgenedp_0.99.5.tar.gz'
>>>>>>>
* installing *source* package ‘cellxgenedp’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cpp11.cpp -o cpp11.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I/usr/local/include -fPIC -Wall -g -O2 -c jsoncons_jmespath.cpp -o jsoncons_jmespath.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 cellxgenedp.so cpp11.o jsoncons_jmespath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2522/bc6926da2349e187eb51661d59cbf92ca3118ea9/libdir/00LOCK-cellxgenedp/00new/cellxgenedp/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 (cellxgenedp)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/cellxgenedp/libs/cellxgenedp.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/cellxgenedp/libs/cellxgenedp.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/cellxgenedp/libs/cellxgenedp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/cellxgenedp/libs/cellxgenedp.so"