merida1 Summary
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Package: sSNAPPY |
Version: 0.99.2 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data sSNAPPY |
BuildTime: 2 minutes 1.00 seconds |
CheckCommand: BiocCheckGitClone('sSNAPPY') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sSNAPPY_0.99.2.tar.gz && BiocCheck('sSNAPPY_0.99.2.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 22.94 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh sSNAPPY_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 1 minutes 54.54 seconds |
PackageFileSize: 2232.30 KiB |
BuildID:: sSNAPPY_20220406122630 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: sSNAPPY. 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 ‘sSNAPPY/DESCRIPTION’ ... OK
* preparing ‘sSNAPPY’:
* 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 ‘sSNAPPY_0.99.2.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('sSNAPPY')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2599/020c9081d0d160ad00fb71be752172405dc27a84/sSNAPPY.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘0.99.2’
* 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 ‘sSNAPPY’ can be installed ... [51s/51s] 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 ... [20s/20s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [16s/16s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
perturbationScore 5.566 0.056 5.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [59s/50s]
[60s/50s] 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('sSNAPPY_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2599/020c9081d0d160ad00fb71be752172405dc27a84/sSNAPPY_0.99.2.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpiySJ81/file13c3e32e7894d/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* 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...
* 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 sSNAPPY...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/compute_ssFC.R (line 87, column 11)
R/normaliseByPermutation.R (line 104, column 37)
R/normaliseByPermutation.R (line 118, column 5)
R/normaliseByPermutation.R (line 121, column 17)
R/pathwayTopology.R (line 73, column 19)
R/pathwayTopology.R (line 74, column 27)
R/pertubationScore.R (line 48, column 31)
R/pertubationScore.R (line 49, column 11)
R/plot_GSnetwork.R (line 78, column 10)
R/plot_GSnetwork.R (line 79, column 9)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/plot_GSnetwork.R (line 45, column 75)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
suppressMessages() in R/pathwayTopology.R (line 95, column 12)
suppressWarnings() in R/pertubationScore.R (line 48, column 5)
* Checking function lengths...
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
weightedAdjMatrix.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
40% of man pages use one of these cases.
Found in the following files:
generate_PermutedScore.Rd
normaliseByPermutation.Rd
perturbationScore.Rd
weightedAdjMatrix.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
generate_PermutedScore.Rd
normaliseByPermutation.Rd
perturbationScore.Rd
weightedAdjMatrix.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; 234 lines (16%) are > 80 characters
long.
First 6 lines:
R/compute_ssFC.R:6 #' The weighted single sample logFCs are ready for c...
R/compute_ssFC.R:14 #' single sample logFCs and mean of logCPM, and the...
R/compute_ssFC.R:15 #' the variance of each mean logCPM value. Gene-wis...
R/compute_ssFC.R:16 #' variances, are then multiplied to single sample ...
R/compute_ssFC.R:19 #' derived. Rownames of the matrix must be genes' e...
R/compute_ssFC.R:22 #' Sample metadata should have the same number of r...
* NOTE: Consider multiples of 4 spaces for line indents, 87
lines(6%) are not.
First 6 lines:
R/normaliseByPermutation.R:131 NB, wei...
R/normaliseByPermutation.R:138 (logCPM[,seq(index[[y]]+1, index[[...
R/pathwayTopology.R:56 "activation_phosphorylation","phospho...
R/pathwayTopology.R:57 "inhibition_dephosphorylation","disso...
R/pathwayTopology.R:58 "activation_dephosphorylation","state...
R/pathwayTopology.R:59 "inhibition_ubiquination","ubiquinati...
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: 10
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
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir sSNAPPY_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘sSNAPPY’ ...
** 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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c code.cpp -o code.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c normaliseByPermutation.cpp -o normaliseByPermutation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ssPertScore.cpp -o ssPertScore.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 sSNAPPY.so RcppExports.o code.o normaliseByPermutation.o ssPertScore.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2599/020c9081d0d160ad00fb71be752172405dc27a84/libdir/00LOCK-sSNAPPY/00new/sSNAPPY/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (sSNAPPY)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/sSNAPPY/libs/sSNAPPY.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/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/sSNAPPY/libs/sSNAPPY.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/sSNAPPY/libs/sSNAPPY.so"
nebbiolo1 Summary
[top]
Package: sSNAPPY |
Version: 0.99.2 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data sSNAPPY |
BuildTime: 1 minutes 19.84 seconds |
CheckCommand: BiocCheckGitClone('sSNAPPY') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings sSNAPPY_0.99.2.tar.gz && BiocCheck('sSNAPPY_0.99.2.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 49.32 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2238.27 KiB |
BuildID:: sSNAPPY_20220406122630 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: sSNAPPY. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* preparing ‘sSNAPPY’:
* 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 ‘sSNAPPY_0.99.2.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('sSNAPPY')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2599/020c9081d0d160ad00fb71be752172405dc27a84/sSNAPPY.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘0.99.2’
* 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 ‘sSNAPPY’ can be installed ... [36s/36s] OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 2.0Mb
* 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 ... [13s/13s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [40s/34s]
[41s/35s] 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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2599/020c9081d0d160ad00fb71be752172405dc27a84/sSNAPPY.Rcheck/00check.log’
for details.
===============================
BiocCheck('sSNAPPY_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2599/020c9081d0d160ad00fb71be752172405dc27a84/sSNAPPY_0.99.2.tar.gz" "/tmp/Rtmp1LPtcm/file34cd57aa632f3/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* 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...
* 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 sSNAPPY...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/compute_ssFC.R (line 87, column 11)
R/normaliseByPermutation.R (line 104, column 37)
R/normaliseByPermutation.R (line 118, column 5)
R/normaliseByPermutation.R (line 121, column 17)
R/pathwayTopology.R (line 73, column 19)
R/pathwayTopology.R (line 74, column 27)
R/pertubationScore.R (line 48, column 31)
R/pertubationScore.R (line 49, column 11)
R/plot_GSnetwork.R (line 78, column 10)
R/plot_GSnetwork.R (line 79, column 9)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/plot_GSnetwork.R (line 45, column 75)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
suppressMessages() in R/pathwayTopology.R (line 95, column 12)
suppressWarnings() in R/pertubationScore.R (line 48, column 5)
* Checking function lengths...
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
weightedAdjMatrix.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
40% of man pages use one of these cases.
Found in the following files:
generate_PermutedScore.Rd
normaliseByPermutation.Rd
perturbationScore.Rd
weightedAdjMatrix.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
generate_PermutedScore.Rd
normaliseByPermutation.Rd
perturbationScore.Rd
weightedAdjMatrix.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; 234 lines (16%) are > 80 characters
long.
First 6 lines:
R/compute_ssFC.R:6 #' The weighted single sample logFCs are ready for c...
R/compute_ssFC.R:14 #' single sample logFCs and mean of logCPM, and the...
R/compute_ssFC.R:15 #' the variance of each mean logCPM value. Gene-wis...
R/compute_ssFC.R:16 #' variances, are then multiplied to single sample ...
R/compute_ssFC.R:19 #' derived. Rownames of the matrix must be genes' e...
R/compute_ssFC.R:22 #' Sample metadata should have the same number of r...
* NOTE: Consider multiples of 4 spaces for line indents, 87
lines(6%) are not.
First 6 lines:
R/normaliseByPermutation.R:131 NB, wei...
R/normaliseByPermutation.R:138 (logCPM[,seq(index[[y]]+1, index[[...
R/pathwayTopology.R:56 "activation_phosphorylation","phospho...
R/pathwayTopology.R:57 "inhibition_dephosphorylation","disso...
R/pathwayTopology.R:58 "activation_dephosphorylation","state...
R/pathwayTopology.R:59 "inhibition_ubiquination","ubiquinati...
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: 10
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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