nebbiolo1 Summary
[top]
| Package: RgnTX |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX |
| BuildTime: 1 minutes 23.43 seconds |
| CheckCommand: BiocCheckGitClone('RgnTX') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings RgnTX_0.99.9.tar.gz && BiocCheck('RgnTX_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 9.95 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3942.42 KiB |
| BuildID:: RgnTX_20220520133533 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RgnTX. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* 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 ‘RgnTX_0.99.9.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('RgnTX')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘0.99.9’
* 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 ‘RgnTX’ can be installed ... [25s/25s] 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 ... [26s/26s] 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 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
shiftedZScoreTx 22.844 0.112 22.956
permTestTxIA 12.577 0.120 12.698
permTestTxIA_customPick 12.576 0.052 12.627
permTestTx 11.170 0.100 11.270
permTestTx_customPick 9.477 0.052 9.529
permTestTx_customAll 8.591 0.024 8.615
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [33s/33s]
[33s/33s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('RgnTX_0.99.9.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/Rtmp8qEoPI/file230b2b52df92e/RgnTX
─ installDir: /tmp/Rtmp8qEoPI/file230b2bbbe43dd
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* 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...
* 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 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 RgnTX...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 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; 522 lines (11%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 103 lines
(2%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the RgnTX.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
| Package: RgnTX |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX |
| BuildTime: 3 minutes 20.35 seconds |
| CheckCommand: BiocCheckGitClone('RgnTX') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RgnTX_0.99.9.tar.gz && BiocCheck('RgnTX_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 11 minutes 20.27 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh RgnTX_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 17.21 seconds |
| PackageFileSize: 3936.91 KiB |
| BuildID:: RgnTX_20220520133533 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RgnTX. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* 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 ‘RgnTX_0.99.9.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('RgnTX')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.9
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘0.99.9’
* 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 ‘RgnTX’ can be installed ... [47s/47s] 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/44s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [262s/262s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shiftedZScoreTx 40.360 0.400 40.758
permTestTxIA_customPick 23.924 0.218 24.139
permTestTxIA 23.559 0.222 23.780
permTestTx 20.169 0.147 20.315
permTestTx_customPick 17.458 0.107 17.564
permTestTx_customAll 15.635 0.116 15.752
overlapCountsTxIA 9.059 0.166 9.226
distanceTx 7.715 0.152 7.867
overlapWidthTx 7.368 0.077 7.446
getStopCodon 7.199 0.102 7.301
randomizeFeaturesTx 6.995 0.087 7.082
getFormatCorrect 6.909 0.068 6.976
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [81s/83s]
[81s/83s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('RgnTX_0.99.9.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: RgnTX
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/RtmpcTuwl6/filee6a243a605e8/RgnTX
─ installDir: /tmp/RtmpcTuwl6/filee6a2457818dd
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2635/e7bfbc77593b4feb2527fa0ca8689c7130f58afa/RgnTX.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* 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...
* 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 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 RgnTX...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 6
functions > 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; 522 lines (11%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 103 lines
(2%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the RgnTX.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 RgnTX_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘RgnTX’ ...
** 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 (RgnTX)