===============================
R CMD BUILD
===============================
* checking for file ‘prozor/DESCRIPTION’ ... OK
* preparing ‘prozor’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘prozor_0.99.3.tar.gz’
===============================
BiocCheckGitClone('prozor')
===============================
This is BiocCheckGitClone version 1.30.0. 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:
prozor.Rproj
* 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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2434/prozor_20211124123804/prozor.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prozor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘prozor’ version ‘0.99.3’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘ssh’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2434/prozor_20211124123804/prozor.Rcheck/00check.log’
for details.
===============================
BiocCheck('prozor_0.99.3.tar.gz')
===============================
This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 4 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
plotFDR (score)
plotFDR (decoy_hit)
plotFDR (qValue_FPR)
plotFDR (qValue_SimpleFDR)
* 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 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 prozor...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.......................................
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
create_fgcz_fasta_db() (R/create_fgcz_fasta_db.R, line 11): 59
lines
readjustWindows() (R/readjustWindow.R, line 53): 54 lines
_anonymous_.123() (R/cdsw.R, line 123): 53 lines
annotateAHO() (R/annotatePeptides.R, line 100): 40 lines
annotatePeptides() (R/annotatePeptides.R, line 43): 30 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
greedyRes2Matrix.Rd, removeSignalPeptide.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
3% of man pages use one of these cases.
Found in the following files:
writeFasta.Rd
* 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; 155 lines (6%) are > 80 characters
long.
First 6 lines:
R/annotatePeptides.R:21 #' @param pepinfo - list of peptides - sequence...
R/annotatePeptides.R:23 #' @param peptide - name of column containing p...
R/annotatePeptides.R:27 #' @return data.frame with columns "peptideSeq"...
R/annotatePeptides.R:33 #' file = system.file("p1000_db1_example/shortf...
R/annotatePeptides.R:83 #' @param pepseq - list of peptides - sequence,...
R/annotatePeptides.R:93 #' file = system.file("p1000_db1_example/shortf...
* NOTE: Consider multiples of 4 spaces for line indents, 194
lines(7%) are not.
First 6 lines:
R/annotatePeptides.R:5 proteinSeq ,
R/annotatePeptides.R:6 proteinID,
R/annotatePeptides.R:7 prefix = "(([RK])|...
R/annotatePeptides.R:8 suffix = "")
R/annotatePeptides.R:44 fasta,
R/annotatePeptides.R:45 peptide = "peptide...
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...
* ERROR: Package must be removed from 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 2
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.