nebbiolo1 Summary
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| Package: spbtest3 |
| Version: 0.99.115 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spbtest3 |
| BuildTime: 0 minutes 7.83 seconds |
| CheckCommand: BiocCheckGitClone('spbtest3') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings spbtest3_0.99.115.tar.gz && BiocCheck('spbtest3_0.99.115.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 13.99 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 476.87 KiB |
| BuildID:: spbtest3_20220328132338 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spbtest3. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* preparing ‘spbtest3’:
* 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 ‘spbtest3_0.99.115.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('spbtest3')
===============================
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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* this is package ‘spbtest3’ version ‘0.99.115’
* 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 ‘spbtest3’ can be installed ... [1s/1s] 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 ... [1s/1s] 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 ... WARNING
Undocumented arguments in documentation object 'test'
‘x’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [0s/1s] 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: 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3.Rcheck/00check.log’
for details.
===============================
BiocCheck('spbtest3_0.99.115.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/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3_0.99.115.tar.gz" "/tmp/RtmpJKYCBW/file3378ba6dde240f/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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in file(s):
test3.Rmd (code line 8, column 18)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in file(s):
vignettes/test.Rnw (code line 4, column 13)
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/spbtest3.Rnw
vignettes/test.Rnw
vignettes/test2.Rmd
vignettes/test3.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest3...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/new_test.R (line 2, column 9)
cat() in R/test.R (line 3, column 5)
print() in R/utils.R (line 4, column 5)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/utils.R (line 7, column 8)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 6
times)
T in R/test.R (line 13, column 7)
T in R/test.R (line 16, column 10)
T in R/test.R (line 20, column 5)
T in R/test.R (line 22, column 21)
T in R/test.R (line 23, column 10)
T in R/utils.R (line 2, column 16)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
utils.R (line 10, column 14)
* WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/test.R (line 30, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
67% of man pages use one of these cases.
Found in the following files:
test.Rd
utils.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
utils.Rd
* 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
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
First 1 lines:
man/test.Rd:12 A simple test function. \code{\link{show}} \code{lin...
* NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
tabs.
First 2 lines:
R/new_test.R:2 cat("This is x",x)
R/new_test.R:3 x + 2
* NOTE: Consider multiples of 4 spaces for line indents, 6
lines(3%) are not.
First 6 lines:
man/test.Rd:25 # test a donttest
man/test.Rd:26 me <- "lori"
man/utils.Rd:19 # test a dontrun
man/utils.Rd:20 a = 1
vignettes/test2.Rmd:5 BiocStyle::html_document:
vignettes/test3.Rmd:5 BiocStyle::html_document:
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 6
NOTE count: 10
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: spbtest3 |
| Version: 0.99.115 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spbtest3 |
| BuildTime: 0 minutes 27.06 seconds |
| CheckCommand: BiocCheckGitClone('spbtest3') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spbtest3_0.99.115.tar.gz && BiocCheck('spbtest3_0.99.115.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 49.83 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh spbtest3_0.99.115.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 4.57 seconds |
| PackageFileSize: 622.83 KiB |
| BuildID:: spbtest3_20220328132338 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spbtest3. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. 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 ‘spbtest3/DESCRIPTION’ ... OK
* preparing ‘spbtest3’:
* 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 ‘spbtest3_0.99.115.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('spbtest3')
===============================
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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* this is package ‘spbtest3’ version ‘0.99.115’
* 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 ‘spbtest3’ can be installed ... [3s/3s] 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 ... [4s/5s] 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 ... WARNING
Undocumented arguments in documentation object 'test'
‘x’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/2s] 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: 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3.Rcheck/00check.log’
for details.
===============================
BiocCheck('spbtest3_0.99.115.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/51/c1bfe9577eb56dd5d0dd3e89a5409ba34c6441e4/spbtest3_0.99.115.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpELZVSi/file185fa40517886/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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in file(s):
test3.Rmd (code line 8, column 18)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in file(s):
vignettes/test.Rnw (code line 4, column 13)
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/spbtest3.Rnw
vignettes/test.Rnw
vignettes/test2.Rmd
vignettes/test3.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest3...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/new_test.R (line 2, column 9)
cat() in R/test.R (line 3, column 5)
print() in R/utils.R (line 4, column 5)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/utils.R (line 7, column 8)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 6
times)
T in R/test.R (line 13, column 7)
T in R/test.R (line 16, column 10)
T in R/test.R (line 20, column 5)
T in R/test.R (line 22, column 21)
T in R/test.R (line 23, column 10)
T in R/utils.R (line 2, column 16)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
utils.R (line 10, column 14)
* WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/test.R (line 30, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
67% of man pages use one of these cases.
Found in the following files:
test.Rd
utils.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
utils.Rd
* 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
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
First 1 lines:
man/test.Rd:12 A simple test function. \code{\link{show}} \code{lin...
* NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
tabs.
First 2 lines:
R/new_test.R:2 cat("This is x",x)
R/new_test.R:3 x + 2
* NOTE: Consider multiples of 4 spaces for line indents, 6
lines(3%) are not.
First 6 lines:
man/test.Rd:25 # test a donttest
man/test.Rd:26 me <- "lori"
man/utils.Rd:19 # test a dontrun
man/utils.Rd:20 a = 1
vignettes/test2.Rmd:5 BiocStyle::html_document:
vignettes/test3.Rmd:5 BiocStyle::html_document:
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 6
NOTE count: 10
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
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir spbtest3_0.99.115.tar.gz'
>>>>>>>
* installing *source* package ‘spbtest3’ ...
** 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 (spbtest3)