Detailed Information does not seem correct
Closed this issue · 1 comments
lshep commented
I'm reviewing a package and ran BiocCheck locally
> library(BiocCheck)
> BiocCheck("octad_0.99.79.tar.gz", 'new_package'=TRUE)
─ BiocCheckVersion: 1.33.0
─ BiocVersion: 3.16
─ Package: octad
─ PackageVersion: 0.99.79
─ sourceDir: /tmp/RtmpM0I6rZ/file1d1363ed5607/octad
─ installDir: /tmp/RtmpM0I6rZ/file1d136f22c755
─ BiocCheckDir: /home/shepherd/PkgReviews/octad.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 version number validity...
Package version 0.99.79; pre-release
* Checking R version dependency...
* NOTE: Update R version dependency from 4.1.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, Normalization, Pathways, Preprocessing, Bayesian,
Clustering, Regression, DNAMethylation, RNASeq, ChIPSeq,
CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation,
DifferentialSplicing, BatchEffect, MultipleComparison,
QualityControl, TimeCourse, ThirdPartyClient, DataImport, GUI
Search 'biocViews' at https://contributions.bioconductor.org
* 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 package installation calls in R code...
* Checking for library/require of octad...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 7
functions > 50 lines.
* Checking man page documentation...
snapshotDate(): 2022-05-17
snapshotDate(): 2022-05-17
* Checking package NEWS...
* 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; 263 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 499 lines
(33%) 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 for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/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 | 10 NOTES
See the octad.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
I wanted to verify and check say
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
When I go into the directory and check the detailed log file ~/PkgReviews/octad.BiocCheck$ cat 00BiocCheck.log The locations given in the check are not accurate
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/octadDrugEnrichment.R (line 26, column 5)
cat() in R/octadDrugEnrichment.R (line 85, column 15)
print() in R/topLineEval.R (line 152, column 3)
print() in R/topLineEval.R (line 153, column 3)
print() in R/topLineEval.R (line 154, column 3)
print() in R/topLineEval.R (line 155, column 3)
Just taking the cat in the first file the line and column locations are wrong. I have included a screen shot with the log output and an emacs open. BiocCheckOffWithLocation.png shows the first entry compared to what was reported. The Example2BadLocation.png my emacs is on the reported location in the file and there is not a cat to be seen
