nebbiolo1 Summary
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Package: xcore |
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 xcore |
BuildTime: 1 minutes 1.20 seconds |
CheckCommand: BiocCheckGitClone('xcore') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings xcore_0.99.5.tar.gz && BiocCheck('xcore_0.99.5.tar.gz', `new-package`=TRUE) |
CheckTime: 6 minutes 8.66 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 1972.82 KiB |
BuildID:: xcore_20220303135711 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: xcore. 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 ‘xcore/DESCRIPTION’ ... OK
* preparing ‘xcore’:
* 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
* building ‘xcore_0.99.5.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('xcore')
===============================
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/2496/536cb0bc34c9ce02fb51704d143e2689c1a88c0a/xcore.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 ‘xcore/DESCRIPTION’ ... OK
* this is package ‘xcore’ 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 whether package ‘xcore’ can be installed ... [13s/13s] 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 ... [14s/14s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [152s/152s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
modelGeneExpression 139.429 0.759 140.197
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [107s/107s]
[107s/107s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocParallel’
* 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/2496/536cb0bc34c9ce02fb51704d143e2689c1a88c0a/xcore.Rcheck/00check.log’
for details.
===============================
BiocCheck('xcore_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/2496/536cb0bc34c9ce02fb51704d143e2689c1a88c0a/xcore_0.99.5.tar.gz" "/tmp/RtmpHn6GB0/file35614614d894d0/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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, ChipOnChip
See http://bioconductor.org/developers/how-to/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 xcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
times)
suppressMessages() in R/processing.R (line 308, column 5)
suppressWarnings() in R/stats.R (line 372, column 26)
suppressWarnings() in R/stats.R (line 440, column 26)
suppressWarnings() in R/stats.R (line 446, column 26)
suppressMessages() in R/stats.R (line 372, column 43)
suppressMessages() in R/stats.R (line 440, column 43)
suppressMessages() in R/stats.R (line 446, column 43)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
modelGeneExpression() (R/stats.R, line 200): 133 lines
modelGeneExpression_ridge_regression_wraper() (R/stats.R, line
354): 52 lines
modelGeneExpression_significance_testing_wraper() (R/stats.R,
line 427): 47 lines
prepareCountsForRegression() (R/processing.R, line 57): 39
lines
_anonymous_.290() (R/stats.R, line 290): 33 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
pipe.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
4% of man pages use one of these cases.
Found in the following files:
design2factor.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
design2factor.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 81 lines (3%) are > 80 characters
long.
First 6 lines:
R/processing.R:4 #' \href{https://bioconductor.org/packages/release/bio...
R/processing.R:6 #' normalized for the library size and transformed int...
R/processing.R:25 #' \item{U}{matrix giving expression values avera...
R/processing.R:63 stopifnot("counts must be an integer matrix" = is.m...
R/processing.R:64 stopifnot("design must be a matrix" = is.matrix(des...
R/processing.R:65 stopifnot("number of rows in design must equal to n...
* NOTE: Consider multiples of 4 spaces for line indents, 474
lines(18%) are not.
First 6 lines:
R/processing.R:58 design,
R/processing.R:59 base_lvl,
R/processing.R:60 log2 = TRUE,
R/processing.R:61 pseudo_count =...
R/processing.R:62 drop_base_lvl ...
R/processing.R:63 stopifnot("counts must be an integer matrix" = is.m...
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: 9
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: xcore |
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 xcore |
BuildTime: 3 minutes 10.83 seconds |
CheckCommand: BiocCheckGitClone('xcore') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xcore_0.99.5.tar.gz && BiocCheck('xcore_0.99.5.tar.gz', `new-package`=TRUE) |
CheckTime: 14 minutes 59.96 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh xcore_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 32.50 seconds |
PackageFileSize: 1968.34 KiB |
BuildID:: xcore_20220303135711 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: xcore. 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: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘xcore/DESCRIPTION’ ... OK
* preparing ‘xcore’:
* 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
* building ‘xcore_0.99.5.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('xcore')
===============================
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/2496/536cb0bc34c9ce02fb51704d143e2689c1a88c0a/xcore.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 ‘xcore/DESCRIPTION’ ... OK
* this is package ‘xcore’ 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 whether package ‘xcore’ can be installed ... [40s/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 ... [44s/71s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [269s/409s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
modelGeneExpression 235.900 2.972 359.636
getCoverage 4.046 0.617 8.082
addSignatures 3.418 0.107 5.613
filterSignatures 3.258 0.112 5.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('xcore_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/2496/536cb0bc34c9ce02fb51704d143e2689c1a88c0a/xcore_0.99.5.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpywrIgQ/file7ed246241a56/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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, ChipOnChip
See http://bioconductor.org/developers/how-to/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 xcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
times)
suppressMessages() in R/processing.R (line 308, column 5)
suppressWarnings() in R/stats.R (line 372, column 26)
suppressWarnings() in R/stats.R (line 440, column 26)
suppressWarnings() in R/stats.R (line 446, column 26)
suppressMessages() in R/stats.R (line 372, column 43)
suppressMessages() in R/stats.R (line 440, column 43)
suppressMessages() in R/stats.R (line 446, column 43)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
modelGeneExpression() (R/stats.R, line 200): 133 lines
modelGeneExpression_ridge_regression_wraper() (R/stats.R, line
354): 52 lines
modelGeneExpression_significance_testing_wraper() (R/stats.R,
line 427): 47 lines
prepareCountsForRegression() (R/processing.R, line 57): 39
lines
_anonymous_.290() (R/stats.R, line 290): 33 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
pipe.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
4% of man pages use one of these cases.
Found in the following files:
design2factor.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
design2factor.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 81 lines (3%) are > 80 characters
long.
First 6 lines:
R/processing.R:4 #' \href{https://bioconductor.org/packages/release/bio...
R/processing.R:6 #' normalized for the library size and transformed int...
R/processing.R:25 #' \item{U}{matrix giving expression values avera...
R/processing.R:63 stopifnot("counts must be an integer matrix" = is.m...
R/processing.R:64 stopifnot("design must be a matrix" = is.matrix(des...
R/processing.R:65 stopifnot("number of rows in design must equal to n...
* NOTE: Consider multiples of 4 spaces for line indents, 474
lines(18%) are not.
First 6 lines:
R/processing.R:58 design,
R/processing.R:59 base_lvl,
R/processing.R:60 log2 = TRUE,
R/processing.R:61 pseudo_count =...
R/processing.R:62 drop_base_lvl ...
R/processing.R:63 stopifnot("counts must be an integer matrix" = is.m...
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: 9
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 xcore_0.99.5.tar.gz'
>>>>>>>
* installing *source* package ‘xcore’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>='
** 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 (xcore)