===============================
BiocCheckGitClone('updateObject')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
inst/scripts/find_serialized_DataFrame_instances-20211119.log
inst/scripts/find_serialized_DataFrame_instances-20220113.log
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* 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/2507/b1a926d65e69f0462ba62ffed8a11eccb6f22287/updateObject.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 ‘updateObject/DESCRIPTION’ ... OK
* this is package ‘updateObject’ version ‘0.99.10’
* 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 ‘updateObject’ 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 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 ... [3s/3s] 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 ... [7s/9s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
updateBiocPackageRepoObjects 4.105 0.316 5.708
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/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: OK
===============================
BiocCheck('updateObject_0.99.10.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/2507/b1a926d65e69f0462ba62ffed8a11eccb6f22287/updateObject_0.99.10.tar.gz" "/tmp/RtmpcXOR3j/file10249d287107ba/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...
* 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 updateObject...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/capture_message.R (line 49, column 13)
cat() in R/git-utils.R (line 59, column 13)
cat() in R/git-utils.R (line 65, column 9)
cat() in R/git-utils.R (line 231, column 5)
cat() in R/git-utils.R (line 263, column 9)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/git-utils.R (line 68, column 14)
R/updateBiocPackageRepoObjects.R (line 35, column 14)
R/updateSerializedObjects.R (line 126, column 17)
R/updateSerializedObjects.R (line 173, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* ERROR: Avoid 'Sys.setenv' (found 6 times)
Sys.setenv() in R/git-utils.R (line 176, column 5)
Sys.setenv() in R/git-utils.R (line 188, column 9)
Sys.setenv() in R/git-utils.R (line 193, column 9)
Sys.setenv() in R/git-utils.R (line 203, column 5)
Sys.setenv() in R/git-utils.R (line 215, column 9)
Sys.setenv() in R/git-utils.R (line 220, column 9)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14
times)
suppressWarnings() in R/git-utils.R (line 26, column 20)
suppressWarnings() in R/git-utils.R (line 49, column 16)
suppressWarnings() in R/git-utils.R (line 51, column 19)
suppressWarnings() in R/git-utils.R (line 56, column 19)
suppressWarnings() in R/updatePackageObjects.R (line 21, column
9)
suppressWarnings() in R/updateSerializedObjects.R (line 64,
column 26)
suppressWarnings() in R/updateSerializedObjects.R (line 86,
column 20)
suppressWarnings() in R/updateSerializedObjects.R (line 95,
column 20)
suppressWarnings() in R/updateSerializedObjects.R (line 151,
column 26)
suppressWarnings() in R/updateSerializedObjects.R (line 169,
column 26)
suppressMessages() in R/updateSerializedObjects.R (line 64,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 85,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 151,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 169,
column 9)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
updateBiocPackageRepoObjects()
(R/updateBiocPackageRepoObjects.R, line 7): 58 lines
update_rda_file() (R/updateSerializedObjects.R, line 146): 53
lines
find_python() (R/find_python.R, line 2): 39 lines
.find_git() (R/git-utils.R, line 8): 31 lines
update_rds_file() (R/updateSerializedObjects.R, line 114): 31
lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
40% of man pages use one of these cases.
Found in the following files:
updateBiocPackageRepoObjects.Rd
updatePackageObjects.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
updateBiocPackageRepoObjects.Rd
updatePackageObjects.Rd
* 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 multiples of 4 spaces for line indents, 284
lines(15%) are not.
First 6 lines:
R/bump_pkg_version.R:52 "to the top-level directory o...
R/bump_pkg_version.R:62 "an R package **source** t...
R/bump_pkg_version.R:65 "it is an R package **inst...
R/bump_pkg_version.R:66 "or the result of extracti...
R/bump_pkg_version.R:81 function(val) paste0(" ", ...
R/find_python.R:14 stop("\n No Python executable can be f...
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: 1
WARNING count: 0
NOTE count: 7
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.