nebbiolo1 Summary
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| Package: single |
| Version: 0.99.16 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data single |
| BuildTime: 0 minutes 41.11 seconds |
| CheckCommand: BiocCheckGitClone('single') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings single_0.99.16.tar.gz && BiocCheck('single_0.99.16.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 10.38 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 956.14 KiB |
| BuildID:: single_20220316144928 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: single. 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: -9. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘single/DESCRIPTION’ ... OK
* preparing ‘single’:
* 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 ‘single_0.99.16.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('single')
===============================
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/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single.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 ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘0.99.16’
* 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 ‘single’ can be installed ... [16s/16s] 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 ... [18s/18s] NOTE
pileup_by_QUAL: no visible binding for global variable ‘count.y’
pileup_by_QUAL: no visible binding for global variable ‘count.x’
pileup_by_QUAL: no visible binding for global variable ‘nucleotide’
pileup_by_QUAL: no visible binding for global variable ‘QUAL’
single_consensus_byBarcode: no visible binding for global variable
‘BCid’
Undefined global functions or variables:
BCid QUAL count.x count.y nucleotide
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [58s/58s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
single_consensus_byBarcode 8.633 0.072 8.706
single_evaluate 8.349 0.060 8.409
evaluate_fits 7.392 0.184 7.576
single_train 7.298 0.108 7.407
fit_logregr 7.155 0.088 7.243
* 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/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single.Rcheck/00check.log’
for details.
===============================
BiocCheck('single_0.99.16.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/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single_0.99.16.tar.gz" "/tmp/RtmpngIug0/file5ed977cacc0b0/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 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...
Warning in remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 14, 2; you may need Sweave2knitr("/tmp/RtmpngIug0/file5ed977b9f9bc3/single/vignettes//single.Rnw") to convert it to knitr
ERROR
TIMEOUT: BiocCheck exceeded 15mins
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: single |
| Version: 0.99.16 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data single |
| BuildTime: 1 minutes 1.05 seconds |
| CheckCommand: BiocCheckGitClone('single') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch single_0.99.16.tar.gz && BiocCheck('single_0.99.16.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 36.59 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh single_0.99.16.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 24.00 seconds |
| PackageFileSize: 947.46 KiB |
| BuildID:: single_20220316144928 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: single. 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 ‘single/DESCRIPTION’ ... OK
* preparing ‘single’:
* 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 ‘single_0.99.16.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('single')
===============================
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/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘0.99.16’
* 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 ‘single’ can be installed ... [24s/24s] 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 ... [25s/25s] NOTE
pileup_by_QUAL: no visible binding for global variable ‘count.y’
pileup_by_QUAL: no visible binding for global variable ‘count.x’
pileup_by_QUAL: no visible binding for global variable ‘nucleotide’
pileup_by_QUAL: no visible binding for global variable ‘QUAL’
single_consensus_byBarcode: no visible binding for global variable
‘BCid’
Undefined global functions or variables:
BCid QUAL count.x count.y nucleotide
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/84s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
single_consensus_byBarcode 13.275 0.088 13.363
single_evaluate 12.837 0.073 12.910
evaluate_fits 11.522 0.129 11.652
single_train 11.395 0.065 11.462
fit_logregr 11.162 0.055 11.216
* 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
‘/Users/pkgbuild/packagebuilder/workers/jobs/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single.Rcheck/00check.log’
for details.
===============================
BiocCheck('single_0.99.16.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/2528/4cba15a70895101ac81e08f013d090d7c89e1807/single_0.99.16.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpfYN0u8/fileaa3d188c1c8c/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 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...
Warning in remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 14, 2; you may need Sweave2knitr("/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpfYN0u8/fileaa3d27a023ba/single/vignettes//single.Rnw") to convert it to knitr
ERROR
TIMEOUT: BiocCheck exceeded 14mins
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir single_0.99.16.tar.gz'
>>>>>>>
* installing *source* package ‘single’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (single)