===============================
BiocCheckGitClone('SUITOR')
===============================
This is BiocCheckGitClone version 1.31.36. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2515/5d97abbae155a5b3a89c8a113590bbd47c623ff4/SUITOR.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SUITOR/DESCRIPTION’ ... OK
* this is package ‘SUITOR’ version ‘0.99.5’
* 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 ‘SUITOR’ can be installed ... [5s/6s] 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 ... [5s/5s] 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
suitor_extract_WH 9.562 0.026 9.589
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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('SUITOR_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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 '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2515/5d97abbae155a5b3a89c8a113590bbd47c623ff4/SUITOR_0.99.5.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp766Laz/file76f953a1ce8d/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 SUITOR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
source_extract_WH.R (line 24, column 47)
source_extract_WH.R (line 28, column 47)
source.R (line 65, column 21)
source.R (line 67, column 24)
source.R (line 71, column 15)
source.R (line 354, column 11)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/source_extract_WH.R (line 84, column 14)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/source.R (line 74, column 29)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/source.R (line 19, column 27)
R/source.R (line 20, column 54)
R/source.R (line 22, column 30)
R/source.R (line 23, column 31)
R/source.R (line 24, column 27)
R/source.R (line 25, column 35)
R/source.R (line 56, column 29)
R/source.R (line 57, column 29)
R/source.R (line 58, column 39)
R/source.R (line 59, column 45)
R/source.R (line 60, column 29)
R/source.R (line 61, column 29)
R/source.R (line 62, column 49)
R/source.R (line 68, column 24)
R/source.R (line 74, column 35)
R/source.R (line 91, column 56)
R/source.R (line 113, column 33)
R/source.R (line 129, column 39)
R/source.R (line 146, column 30)
R/source.R (line 157, column 30)
R/source.R (line 214, column 27)
R/source.R (line 414, column 22)
R/source.R (line 419, column 10)
R/source.R (line 423, column 39)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
check_op() (R/source.R, line 24): 60 lines
getSummary() (R/source.R, line 260): 60 lines
default.list() (R/source.R, line 343): 49 lines
suitor_seq_C() (R/source.R, line 214): 46 lines
set_op_par() (R/source.R, line 84): 35 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
suitor.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
suitor.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; 119 lines (10%) are > 80 characters
long.
First 6 lines:
R/source_extract_WH.R:44 clusterExport(cl=clus, c("extractWH_seq_...
R/source_extract_WH.R:112 ret <- foreach(i=seq_len(n), .verbose=FAL...
R/source.R:20 if (!is.matrix(data) && !is.data.frame(data)) stop("ERR...
R/source.R:58 if (op$min.rank > op$max.rank) stop("ERROR with option ...
R/source.R:74 if (op$min.rank > m) stop(paste("ERROR: option min.rank...
R/source.R:178 tmp <- .C("C_call_nmf", as.numeric(x), as.integer(ia...
* NOTE: Consider multiples of 4 spaces for line indents, 437
lines(38%) are not.
First 6 lines:
R/source_extract_WH.R:3
R/source_extract_WH.R:4 data <- check_data(data)
R/source_extract_WH.R:5 nr <- nrow(data)
R/source_extract_WH.R:6 nc <- ncol(data)
R/source_extract_WH.R:7 if (!is.list(op)) op <- list()
R/source_extract_WH.R:8 op$min.rank <- rank
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: 9
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