nebbiolo1 Summary
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| Package: partCNV |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data partCNV |
| BuildTime: 0 minutes 56.76 seconds |
| CheckCommand: BiocCheckGitClone('partCNV') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2861/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.install-out.txt partCNV_0.99.2.tar.gz && BiocCheck('partCNV_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 56.13 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1949.80 KiB |
| BuildID:: partCNV_20230130213953 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: partCNV. 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: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* preparing ‘partCNV’:
* 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
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘partCNV/data/Hg38_gtf.RData’ ‘partCNV/data/SimData.RData’
* building ‘partCNV_0.99.2.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('partCNV')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV
─ 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/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ 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 ‘partCNV’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/10s] OK
* checking loading without being on the library search path ... [7s/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 ... [20s/20s] NOTE
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
data
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GetExprCountCyto.Rd':
\examples lines wider than 100 characters:
GetExprCountCyto(cytoloc_output = res, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNV.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNVH.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
These lines will be truncated in the PDF manual.
* 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 ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [46s/48s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetCytoLocation 10.209 2.273 13.849
partCNVH 8.206 0.508 9.017
partCNV 7.949 0.755 9.008
GetExprCountCyto 4.405 0.876 5.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [34s/36s]
[34s/36s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.Rcheck/00check.log’
for details.
===============================
BiocCheck('partCNV_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/Rtmpk3coGP/file3535673396fff6/partCNV
─ installDir: /tmp/Rtmpk3coGP/file35356714bd2fea
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.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 3.5.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for 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 partCNV...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* 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; 106 lines (12%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 26 lines
(3%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
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 ──
1 ERRORS | 0 WARNINGS | 5 NOTES
See the partCNV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: partCNV |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data partCNV |
| BuildTime: 2 minutes 1.48 seconds |
| CheckCommand: BiocCheckGitClone('partCNV') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2861/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.install-out.txt partCNV_0.99.2.tar.gz && BiocCheck('partCNV_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 37.37 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh partCNV_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 46.16 seconds |
| PackageFileSize: 1966.46 KiB |
| BuildID:: partCNV_20230130213953 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: partCNV. 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: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* preparing ‘partCNV’:
* 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
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘partCNV/data/Hg38_gtf.RData’ ‘partCNV/data/SimData.RData’
* building ‘partCNV_0.99.2.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('partCNV')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV
─ 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/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ 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 ‘partCNV’ 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 ... [13s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/13s] OK
* checking whether the package can be unloaded cleanly ... [12s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/14s] OK
* checking loading without being on the library search path ... [13s/14s] 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 ... [42s/45s] NOTE
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
data
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GetExprCountCyto.Rd':
\examples lines wider than 100 characters:
GetExprCountCyto(cytoloc_output = res, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNV.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
Rd file 'partCNVH.Rd':
\examples lines wider than 100 characters:
exprout <- GetExprCountCyto(cytoloc_output = cytoloc, Counts = as.matrix(SimData), normalization = TRUE, qt_cutoff = 0.99)
These lines will be truncated in the PDF manual.
* 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 ... [4s/5s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [72s/88s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
partCNV 14.941 0.696 17.781
partCNVH 14.563 0.544 17.562
GetCytoLocation 12.913 1.408 22.716
GetExprCountCyto 7.235 0.816 8.968
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [61s/69s]
[61s/69s] 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 ... [9s/9s] OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.Rcheck/00check.log’
for details.
===============================
BiocCheck('partCNV_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: partCNV
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpcRm4mT/filec89d167a9d92/partCNV
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpcRm4mT/filec89d4c225d7d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2861/e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1/partCNV.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 3.5.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for 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 partCNV...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* 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; 106 lines (12%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 26 lines
(3%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
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 ──
1 ERRORS | 0 WARNINGS | 5 NOTES
See the partCNV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir partCNV_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘partCNV’ ...
** using staged installation
** R
** data
** 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 (partCNV)