nebbiolo2 Summary
[top]
| Package: MSstatsBig |
| Version: 0.99.7 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsBig |
| BuildTime: 0 minutes 12.79 seconds |
| CheckCommand: BiocCheckGitClone('MSstatsBig') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3193/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.install-out.txt MSstatsBig_0.99.7.tar.gz && BiocCheck('MSstatsBig_0.99.7.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 3.57 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 70.02 KiB |
| BuildID:: MSstatsBig_20231017105542 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MSstatsBig. 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. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* preparing ‘MSstatsBig’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘MSstatsBig_0.99.7.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('MSstatsBig')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: MSstatsBig
─ PackageVersion: 0.99.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsBig’ version ‘0.99.7’
* 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 ‘MSstatsBig’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] 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 ... [3s/3s] 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] NOTE
MSstatsPreprocessBig: no visible binding for global variable ‘input’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘PeptideSequence’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘PrecursorCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘FragmentIon’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘ProductCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘ProteinName’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Feature’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Intensity’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘MeanAbundance’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘feature_rank’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘NumProteins’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘IsotopeLabelType’
MSstatsPreprocessBigArrow: no visible binding for global variable ‘Run’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Condition’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘BioReplicate’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘%>%’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Condition’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘BioReplicate’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘PeptideSequence’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘n_distinct’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘ProteinName’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘NumProteins’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘tbl’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘PrecursorCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘FragmentIon’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘ProductCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘IsotopeLabelType’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Run’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Intensity’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘min_rank’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Rank’
cleanSpectronautChunk: no visible global function definition for
‘all_of’
cleanSpectronautChunk: no visible binding for global variable
‘Intensity’
cleanSpectronautChunk: no visible binding for global variable
‘Excluded’
cleanSpectronautChunk: no visible binding for global variable
‘Identified’
cleanSpectronautChunk: no visible binding for global variable
‘EGQvalue’
cleanSpectronautChunk: no visible binding for global variable
‘PGQvalue’
cleanSpectronautChunk: no visible binding for global variable
‘FFrgLossType’
cleanSpectronautChunk: no visible binding for global variable
‘LabeledSequence’
cleanSpectronautChunk: no visible global function definition for ‘:=’
cleanSpectronautChunk: no visible binding for global variable
‘IsotopeLabelType’
cleanSpectronautChunk: no visible global function definition for
‘if_else’
cleanSpectronautChunk: no visible binding for global variable
‘IsLabeled’
cleanSpectronautChunk: no visible binding for global variable
‘ProteinName’
cleanSpectronautChunk: no visible binding for global variable
‘PeptideSequence’
cleanSpectronautChunk: no visible binding for global variable
‘PrecursorCharge’
cleanSpectronautChunk: no visible binding for global variable
‘FragmentIon’
cleanSpectronautChunk: no visible binding for global variable
‘ProductCharge’
cleanSpectronautChunk: no visible binding for global variable ‘Run’
cleanSpectronautChunk: no visible binding for global variable
‘BioReplicate’
cleanSpectronautChunk: no visible binding for global variable
‘Condition’
Undefined global functions or variables:
%>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature
FragmentIon Identified Intensity IsLabeled IsotopeLabelType
LabeledSequence MeanAbundance NumObs NumProteins PGQvalue
PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run
all_of feature_rank if_else input min_rank n_distinct tbl
* 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 files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.Rcheck/00check.log’
for details.
===============================
BiocCheck('MSstatsBig_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: MSstatsBig
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/Rtmp43Lx1K/file10deb75205cc90/MSstatsBig
─ installDir: /tmp/Rtmp43Lx1K/file10deb71f88a8b3
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.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...
* 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:
Preprocessing
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...
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MSstatsBig...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 62 lines (8%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 257 lines
(32%) 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...
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the MSstatsBig.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: MSstatsBig |
| Version: 0.99.7 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsBig |
| BuildTime: 0 minutes 9.64 seconds |
| CheckCommand: BiocCheckGitClone('MSstatsBig') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3193/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.install-out.txt MSstatsBig_0.99.7.tar.gz && BiocCheck('MSstatsBig_0.99.7.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 51.70 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MSstatsBig_0.99.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 6.41 seconds |
| PackageFileSize: 69.90 KiB |
| BuildID:: MSstatsBig_20231017105542 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MSstatsBig. 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. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* preparing ‘MSstatsBig’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘MSstatsBig_0.99.7.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('MSstatsBig')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: MSstatsBig
─ PackageVersion: 0.99.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsBig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsBig’ version ‘0.99.7’
* 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 ‘MSstatsBig’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [6s/7s] NOTE
MSstatsPreprocessBig: no visible binding for global variable ‘input’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘PeptideSequence’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘PrecursorCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘FragmentIon’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘ProductCharge’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘ProteinName’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Feature’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Intensity’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘MeanAbundance’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘feature_rank’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘NumProteins’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘IsotopeLabelType’
MSstatsPreprocessBigArrow: no visible binding for global variable ‘Run’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘Condition’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘BioReplicate’
MSstatsPreprocessBigArrow: no visible binding for global variable
‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘%>%’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Condition’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘BioReplicate’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘PeptideSequence’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘n_distinct’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘ProteinName’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘NumProteins’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘tbl’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘PrecursorCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘FragmentIon’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘ProductCharge’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘IsotopeLabelType’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Run’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Intensity’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘NumObs’
MSstatsPreprocessBigSparklyr: no visible global function definition for
‘min_rank’
MSstatsPreprocessBigSparklyr: no visible binding for global variable
‘Rank’
cleanSpectronautChunk: no visible global function definition for
‘all_of’
cleanSpectronautChunk: no visible binding for global variable
‘Intensity’
cleanSpectronautChunk: no visible binding for global variable
‘Excluded’
cleanSpectronautChunk: no visible binding for global variable
‘Identified’
cleanSpectronautChunk: no visible binding for global variable
‘EGQvalue’
cleanSpectronautChunk: no visible binding for global variable
‘PGQvalue’
cleanSpectronautChunk: no visible binding for global variable
‘FFrgLossType’
cleanSpectronautChunk: no visible binding for global variable
‘LabeledSequence’
cleanSpectronautChunk: no visible global function definition for ‘:=’
cleanSpectronautChunk: no visible binding for global variable
‘IsotopeLabelType’
cleanSpectronautChunk: no visible global function definition for
‘if_else’
cleanSpectronautChunk: no visible binding for global variable
‘IsLabeled’
cleanSpectronautChunk: no visible binding for global variable
‘ProteinName’
cleanSpectronautChunk: no visible binding for global variable
‘PeptideSequence’
cleanSpectronautChunk: no visible binding for global variable
‘PrecursorCharge’
cleanSpectronautChunk: no visible binding for global variable
‘FragmentIon’
cleanSpectronautChunk: no visible binding for global variable
‘ProductCharge’
cleanSpectronautChunk: no visible binding for global variable ‘Run’
cleanSpectronautChunk: no visible binding for global variable
‘BioReplicate’
cleanSpectronautChunk: no visible binding for global variable
‘Condition’
Undefined global functions or variables:
%>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature
FragmentIon Identified Intensity IsLabeled IsotopeLabelType
LabeledSequence MeanAbundance NumObs NumProteins PGQvalue
PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run
all_of feature_rank if_else input min_rank n_distinct tbl
* 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 files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.Rcheck/00check.log’
for details.
===============================
BiocCheck('MSstatsBig_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: MSstatsBig
─ PackageVersion: 0.99.7
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpt8sON2/file3a132a2db58d/MSstatsBig
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpt8sON2/file3a1329942a46
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3193/831fa8c77dcc886ef4240f35275b6a1cb1740f85/MSstatsBig.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...
* 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:
Preprocessing
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...
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MSstatsBig...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 62 lines (8%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 257 lines
(32%) 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...
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the MSstatsBig.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MSstatsBig_0.99.7.tar.gz'
>>>>>>>
* installing *source* package ‘MSstatsBig’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsBig)