===============================
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_0.99.29.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_20211005134139/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 ‘0.99.29’
* 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 ... [30s/30s] 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 ... [30s/30s] 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 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 ... [55s/52s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [32s/31s]
[32s/31s] 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('comapr_0.99.29.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/RtmpJGn5g5/file1dd83b7f2c3ee8/comapr/R/count-gt.R (line
102, column 11)
/tmp/RtmpJGn5g5/file1dd83b7f2c3ee8/comapr/R/count-gt.R (line
103, column 11)
/tmp/RtmpJGn5g5/file1dd83b7f2c3ee8/comapr/R/count-gt.R (line
132, column 21)
/tmp/RtmpJGn5g5/file1dd83b7f2c3ee8/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 88, column 3)
suppressMessages() in R/read-hap-state.R (line 154, column 3)
* Checking function lengths.................................................
* NOTE: Recommended function length <= 50 lines.
There are 12 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 139): 94 lines
plotGeneticDist() (R/plot-genetic-dist.R, line 36): 72 lines
plot_count() (R/plot-count.R, line 163): 64 lines
permuteDist() (R/bootstrap.R, line 85): 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; 101 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, 1280
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 result_fun <- function(){
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