===============================
R CMD BUILD
===============================
* checking for file ‘comapr/DESCRIPTION’ ... OK
* preparing ‘comapr’:
* 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 ‘comapr_0.99.25.tar.gz’
===============================
BiocCheckGitClone('comapr')
===============================
This is BiocCheckGitClone version 1.29.14. 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...
* Checking CITATION...
Summary:
ERROR count: 0
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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2335/comapr_20210927163712/comapr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘comapr/DESCRIPTION’ ... OK
* this is package ‘comapr’ version ‘0.99.25’
* 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 ‘comapr’ can be installed ... [34s/34s] 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 ... [31s/31s] 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 'getAFTracks'
‘chunk’
Undocumented arguments in documentation object 'getCellAFTrack'
‘chunk’
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/38s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [29s/28s]
[29s/28s] 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/2335/comapr_20210927163712/comapr.Rcheck/00check.log’
for details.
===============================
BiocCheck('comapr_0.99.25.tar.gz')
===============================
This is BiocCheck version 1.29.14. 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...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.1.0.
* 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...
* 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 comapr...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/Rtmp5BjHkw/file3ab5ae585dc4dc/comapr/R/count-gt.R (line
102, column 11)
/tmp/Rtmp5BjHkw/file3ab5ae585dc4dc/comapr/R/count-gt.R (line
103, column 11)
/tmp/Rtmp5BjHkw/file3ab5ae585dc4dc/comapr/R/count-gt.R (line
132, column 21)
/tmp/Rtmp5BjHkw/file3ab5ae585dc4dc/comapr/R/count-gt.R (line
134, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
suppressMessages() in R/diagnostic-qc-checks.R (line 139,
column 14)
suppressMessages() in R/plot-count.R (line 189, column 7)
suppressMessages() in R/plot-count.R (line 204, column 7)
suppressWarnings() in R/read-hap-state.R (line 84, column 3)
suppressMessages() in R/read-hap-state.R (line 150, column 3)
* Checking function lengths.................................................
* NOTE: Recommended function length <= 50 lines.
There are 11 functions > 50 lines.
The longest 5 functions are:
readColMM() (R/read-col-mm.R, line 23): 145 lines
.filterCOsExtra() (R/read-hap-state.R, line 135): 95 lines
plotGeneticDist() (R/plot-genetic-dist.R, line 36): 70 lines
plot_count() (R/plot-count.R, line 163): 64 lines
plotMissingGT() (R/count-gt.R, line 176): 63 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
countBinState.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:
countBinState.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 shorter lines; 99 lines (2%) are > 80 characters
long.
First 6 lines:
R/cal-genetic-dist.R:291 rowMeans(as.ma...
R/cal-genetic-dist.R:327 rowMeans(as.ma...
R/combineHapState.R:9 #' @importFrom SummarizedExperiment rowRanges ass...
R/combineHapState.R:50 t[se1_rows,seq_len(ncol(rse1))] <- SummarizedE...
R/count-co.R:16 #' @importFrom GenomicRanges GRanges seqnames mcols ran...
R/count-co.R:100 # len_prop <- overlapsRanges(query = ranges(gp...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
R/read-col-mm.R:56 stop("readMM(): row values 'i' are not in 1:n...
* NOTE: Consider multiples of 4 spaces for line indents, 1266
lines(24%) are not.
First 6 lines:
R/bootstrap.R:34 grep(gp, colData(co_gr)[, gr...
R/bootstrap.R:36 count_matrix <- as.matrix(mcols(co_gr))
R/bootstrap.R:37 group_idx <- lapply(group_by, function(gp){
R/bootstrap.R:40 }
R/bootstrap.R:42 #group_size <- sapply(group_idx, length)
R/bootstrap.R:43 boots_result <- BiocParallel::bplapply(seq_len(B), 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: 0
WARNING count: 0
NOTE count: 10
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