===============================
BiocCheckGitClone('seqpac')
===============================
This is BiocCheckGitClone version 1.31.30. 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...
* Checking that provided CITATION file is correctly formatted...
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
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2275/0138aa29d65f0b5597adfb6067879d87dae7ec89/seqpac.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.4’
* 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 ‘seqpac’ can be installed ... [10s/10s] OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
doc 1.7Mb
extdata 3.4Mb
* 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 ... [16s/16s] OK
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12m/10m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PAC_gtf 161.582 3.009 98.004
make_counts 70.812 4.843 67.647
PAC_deseq 47.975 0.352 48.335
add_reanno 36.688 5.992 32.993
make_reanno 35.909 6.097 32.118
map_reanno 35.879 6.093 32.104
make_pheno 25.921 5.074 21.875
make_PAC 26.076 3.908 21.967
PAC_covplot 22.769 0.388 23.178
make_cutadapt 21.563 0.254 21.816
make_trim 21.114 0.362 21.475
PAC_mapper 20.997 0.287 21.306
simplify_reanno 11.733 1.810 11.995
reanno 11.320 1.802 11.561
as.reanno 10.417 1.741 10.627
names 9.061 1.820 9.306
overview 8.883 1.775 9.085
tRNA_class 8.600 1.735 9.964
full 8.536 1.692 8.686
PAC_trna 8.501 1.683 9.820
PAC_pca 7.526 0.115 7.656
PAC_jitter 7.063 0.146 7.221
PAC_nbias 7.172 0.023 7.197
map_rangetype 4.012 1.583 5.210
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('seqpac_0.99.4.tar.gz')
===============================
This is BiocCheck version 1.31.30. 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/2275/0138aa29d65f0b5597adfb6067879d87dae7ec89/seqpac_0.99.4.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpEH8TMK/file497b3e083688/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...
* 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...
Workflow
* 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...
* WARNING: Import mcols, as, new, setMethod, terms.formula in
DESCRIPTION as well as NAMESPACE.
* 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 seqpac...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
add_reanno.R (line 264, column 15)
add_reanno.R (line 269, column 17)
add_reanno.R (line 319, column 16)
add_reanno.R (line 343, column 17)
add_reanno.R (line 464, column 49)
add_reanno.R (line 468, column 55)
filtsep_bin.R (line 68, column 12)
import_reanno.R (line 137, column 13)
import_reanno.R (line 201, column 51)
make_conv.R (line 157, column 12)
make_conv.R (line 192, column 14)
make_conv.R (line 229, column 12)
make_conv.R (line 291, column 14)
make_counts.R (line 369, column 35)
make_counts.R (line 455, column 35)
make_counts.R (line 522, column 40)
make_cutadapt.R (line 172, column 37)
make_pheno.R (line 199, column 16)
make_pheno.R (line 206, column 16)
make_reanno.R (line 230, column 16)
make_reanno.R (line 232, column 12)
make_reanno.R (line 283, column 14)
make_reanno.R (line 288, column 18)
make_reanno.R (line 315, column 15)
make_trim.R (line 242, column 42)
make_trim.R (line 300, column 7)
make_trim.R (line 409, column 18)
make_trim.R (line 619, column 53)
make_trim.R (line 649, column 14)
make_trim.R (line 662, column 12)
map_rangetype.R (line 129, column 48)
map_rangetype.R (line 152, column 14)
map_rangetype.R (line 225, column 17)
map_rangetype.R (line 312, column 14)
map_rangetype.R (line 377, column 17)
map_rangetype.R (line 383, column 17)
map_reanno.R (line 361, column 12)
map_reanno.R (line 371, column 15)
merge_lanes.R (line 142, column 30)
merge_lanes.R (line 150, column 14)
PAC_check.R (line 118, column 52)
PAC_check.R (line 127, column 54)
PAC_covplot.R (line 219, column 14)
PAC_covplot.R (line 238, column 14)
PAC_covplot.R (line 262, column 12)
PAC_covplot.R (line 268, column 36)
PAC_covplot.R (line 272, column 30)
PAC_covplot.R (line 280, column 54)
PAC_covplot.R (line 301, column 12)
PAC_deseq.R (line 131, column 13)
PAC_filter.R (line 253, column 17)
PAC_gtf.R (line 142, column 21)
PAC_gtf.R (line 160, column 13)
PAC_gtf.R (line 279, column 12)
PAC_gtf.R (line 304, column 12)
PAC_gtf.R (line 355, column 36)
PAC_gtf.R (line 386, column 12)
PAC_gtf.R (line 392, column 39)
PAC_gtf.R (line 437, column 14)
PAC_gtf.R (line 441, column 16)
PAC_gtf.R (line 453, column 14)
PAC_gtf.R (line 457, column 16)
PAC_jitter.R (line 167, column 22)
PAC_mapper.R (line 260, column 12)
PAC_mapper.R (line 320, column 12)
PAC_mapper.R (line 358, column 49)
PAC_nbias.R (line 186, column 12)
PAC_norm.R (line 61, column 15)
PAC_pca.R (line 129, column 47)
PAC_pie.R (line 167, column 15)
PAC_pie.R (line 181, column 13)
PAC_pie.R (line 193, column 24)
PAC_pie.R (line 193, column 40)
PAC_saturation.R (line 86, column 41)
PAC_saturation.R (line 102, column 14)
PAC_saturation.R (line 188, column 35)
PAC_sizedist.R (line 174, column 14)
PAC_sizedist.R (line 197, column 12)
PAC_stackbar.R (line 153, column 15)
PAC_stackbar.R (line 167, column 13)
PAC_summary.R (line 144, column 50)
PAC_trna.R (line 339, column 23)
PAC_trna.R (line 359, column 16)
simplify_reanno.R (line 202, column 23)
simplify_reanno.R (line 264, column 15)
simplify_reanno.R (line 282, column 12)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/add_reanno.R (line 250, column 3)
cat() in R/add_reanno.R (line 253, column 5)
cat() in R/add_reanno.R (line 261, column 5)
cat() in R/add_reanno.R (line 281, column 9)
cat() in R/add_reanno.R (line 313, column 5)
cat() in R/add_reanno.R (line 333, column 5)
cat() in R/add_reanno.R (line 386, column 13)
cat() in R/add_reanno.R (line 425, column 9)
cat() in R/add_reanno.R (line 436, column 5)
cat() in R/add_reanno.R (line 485, column 5)
cat() in R/import_reanno.R (line 130, column 3)
cat() in R/import_reanno.R (line 138, column 5)
cat() in R/import_reanno.R (line 178, column 9)
cat() in R/import_reanno.R (line 186, column 9)
cat() in R/import_reanno.R (line 245, column 5)
cat() in R/make_conv.R (line 121, column 3)
cat() in R/make_conv.R (line 132, column 3)
cat() in R/make_conv.R (line 143, column 7)
cat() in R/make_conv.R (line 155, column 3)
cat() in R/make_conv.R (line 190, column 5)
cat() in R/make_conv.R (line 225, column 3)
cat() in R/make_conv.R (line 305, column 3)
cat() in R/make_counts.R (line 195, column 3)
cat() in R/make_counts.R (line 208, column 5)
cat() in R/make_counts.R (line 210, column 5)
cat() in R/make_counts.R (line 212, column 3)
cat() in R/make_counts.R (line 231, column 5)
cat() in R/make_counts.R (line 232, column 5)
cat() in R/make_counts.R (line 233, column 5)
cat() in R/make_counts.R (line 234, column 5)
cat() in R/make_counts.R (line 251, column 7)
cat() in R/make_counts.R (line 252, column 7)
cat() in R/make_counts.R (line 253, column 7)
cat() in R/make_counts.R (line 255, column 7)
cat() in R/make_counts.R (line 256, column 7)
cat() in R/make_counts.R (line 258, column 7)
cat() in R/make_counts.R (line 280, column 5)
cat() in R/make_counts.R (line 281, column 5)
cat() in R/make_counts.R (line 282, column 5)
cat() in R/make_counts.R (line 283, column 5)
cat() in R/make_counts.R (line 302, column 7)
cat() in R/make_counts.R (line 303, column 7)
cat() in R/make_counts.R (line 304, column 7)
cat() in R/make_counts.R (line 305, column 7)
cat() in R/make_counts.R (line 307, column 7)
cat() in R/make_counts.R (line 308, column 7)
cat() in R/make_counts.R (line 310, column 7)
cat() in R/make_counts.R (line 311, column 7)
cat() in R/make_counts.R (line 313, column 7)
cat() in R/make_counts.R (line 314, column 7)
cat() in R/make_counts.R (line 316, column 7)
cat() in R/make_counts.R (line 353, column 3)
cat() in R/make_counts.R (line 390, column 3)
cat() in R/make_counts.R (line 422, column 5)
cat() in R/make_counts.R (line 439, column 5)
cat() in R/make_counts.R (line 443, column 7)
cat() in R/make_counts.R (line 445, column 7)
cat() in R/make_counts.R (line 482, column 3)
print() in R/make_counts.R (line 213, column 3)
print() in R/make_counts.R (line 254, column 7)
print() in R/make_counts.R (line 257, column 7)
print() in R/make_counts.R (line 306, column 7)
print() in R/make_counts.R (line 309, column 7)
print() in R/make_counts.R (line 312, column 7)
print() in R/make_counts.R (line 315, column 7)
print() in R/make_counts.R (line 580, column 5)
cat() in R/make_cutadapt.R (line 135, column 3)
cat() in R/make_cutadapt.R (line 136, column 3)
cat() in R/make_pheno.R (line 221, column 5)
cat() in R/make_pheno.R (line 226, column 7)
cat() in R/make_pheno.R (line 228, column 5)
cat() in R/make_pheno.R (line 236, column 5)
cat() in R/make_pheno.R (line 256, column 5)
cat() in R/make_pheno.R (line 261, column 3)
print() in R/make_pheno.R (line 229, column 5)
cat() in R/make_reanno.R (line 243, column 3)
cat() in R/make_reanno.R (line 301, column 3)
cat() in R/make_reanno.R (line 334, column 5)
cat() in R/make_reanno.R (line 354, column 7)
cat() in R/make_reanno.R (line 358, column 7)
cat() in R/make_reanno.R (line 360, column 7)
cat() in R/make_reanno.R (line 368, column 7)
cat() in R/make_trim.R (line 225, column 5)
cat() in R/make_trim.R (line 230, column 7)
cat() in R/make_trim.R (line 234, column 5)
cat() in R/make_trim.R (line 244, column 5)
cat() in R/make_trim.R (line 260, column 5)
cat() in R/make_trim.R (line 295, column 3)
cat() in R/make_trim.R (line 296, column 3)
cat() in R/map_rangetype.R (line 271, column 7)
cat() in R/map_rangetype.R (line 286, column 7)
cat() in R/map_rangetype.R (line 292, column 7)
print() in R/map_rangetype.R (line 294, column 7)
cat() in R/map_reanno.R (line 308, column 7)
cat() in R/map_reanno.R (line 345, column 5)
cat() in R/map_reanno.R (line 346, column 5)
cat() in R/map_reanno.R (line 347, column 5)
cat() in R/map_reanno.R (line 348, column 5)
cat() in R/map_reanno.R (line 355, column 5)
cat() in R/map_reanno.R (line 356, column 5)
cat() in R/map_reanno.R (line 357, column 5)
cat() in R/map_reanno.R (line 362, column 5)
cat() in R/map_reanno.R (line 363, column 5)
cat() in R/map_reanno.R (line 365, column 5)
cat() in R/map_reanno.R (line 372, column 7)
cat() in R/map_reanno.R (line 382, column 9)
cat() in R/map_reanno.R (line 395, column 9)
cat() in R/map_reanno.R (line 430, column 25)
cat() in R/map_reanno.R (line 433, column 11)
cat() in R/map_reanno.R (line 434, column 5)
cat() in R/map_reanno.R (line 436, column 3)
cat() in R/map_reanno.R (line 437, column 3)
cat() in R/map_reanno.R (line 442, column 3)
cat() in R/map_reanno.R (line 443, column 3)
cat() in R/PAC_covplot.R (line 196, column 3)
cat() in R/PAC_covplot.R (line 201, column 3)
cat() in R/PAC_covplot.R (line 204, column 7)
cat() in R/PAC_covplot.R (line 207, column 7)
print() in R/PAC_covplot.R (line 208, column 7)
print() in R/PAC_covplot.R (line 227, column 5)
cat() in R/PAC_deseq.R (line 118, column 3)
cat() in R/PAC_deseq.R (line 167, column 3)
cat() in R/PAC_deseq.R (line 168, column 3)
cat() in R/PAC_deseq.R (line 169, column 3)
cat() in R/PAC_deseq.R (line 170, column 3)
cat() in R/PAC_deseq.R (line 173, column 15)
cat() in R/PAC_deseq.R (line 176, column 5)
print() in R/PAC_deseq.R (line 178, column 5)
print() in R/PAC_deseq.R (line 233, column 3)
cat() in R/PAC_filter.R (line 133, column 7)
cat() in R/PAC_filter.R (line 178, column 7)
cat() in R/PAC_filter.R (line 206, column 7)
cat() in R/PAC_filter.R (line 219, column 7)
cat() in R/PAC_filter.R (line 222, column 7)
cat() in R/PAC_filter.R (line 288, column 7)
cat() in R/PAC_filter.R (line 300, column 7)
print() in R/PAC_filter.R (line 286, column 7)
cat() in R/PAC_gtf.R (line 145, column 3)
cat() in R/PAC_gtf.R (line 195, column 7)
cat() in R/PAC_gtf.R (line 202, column 9)
cat() in R/PAC_gtf.R (line 274, column 3)
cat() in R/PAC_gtf.R (line 299, column 3)
cat() in R/PAC_gtf.R (line 315, column 7)
cat() in R/PAC_gtf.R (line 326, column 7)
cat() in R/PAC_gtf.R (line 327, column 7)
cat() in R/PAC_gtf.R (line 337, column 3)
cat() in R/PAC_gtf.R (line 388, column 5)
cat() in R/PAC_gtf.R (line 434, column 5)
cat() in R/PAC_gtf.R (line 438, column 7)
cat() in R/PAC_gtf.R (line 450, column 5)
cat() in R/PAC_gtf.R (line 454, column 7)
cat() in R/PAC_mapper.R (line 168, column 5)
cat() in R/PAC_mapper.R (line 172, column 7)
cat() in R/PAC_mapper.R (line 176, column 9)
cat() in R/PAC_mapper.R (line 222, column 5)
cat() in R/PAC_mapper.R (line 228, column 7)
cat() in R/PAC_mapper.R (line 229, column 7)
print() in R/PAC_mapper.R (line 279, column 9)
print() in R/PAC_mapper.R (line 288, column 9)
cat() in R/PAC_nbias.R (line 149, column 4)
print() in R/PAC_pca.R (line 221, column 3)
print() in R/PAC_pie.R (line 256, column 5)
cat() in R/PAC_saturation.R (line 71, column 3)
cat() in R/PAC_saturation.R (line 80, column 3)
cat() in R/PAC_saturation.R (line 82, column 3)
cat() in R/PAC_saturation.R (line 84, column 3)
cat() in R/PAC_saturation.R (line 122, column 3)
cat() in R/PAC_trna.R (line 443, column 12)
cat() in R/seqpac_generics_methods.R (line 366, column 3)
cat() in R/seqpac_generics_methods.R (line 367, column 3)
cat() in R/seqpac_generics_methods.R (line 368, column 3)
cat() in R/seqpac_generics_methods.R (line 374, column 3)
cat() in R/seqpac_generics_methods.R (line 375, column 3)
cat() in R/seqpac_generics_methods.R (line 376, column 3)
cat() in R/seqpac_generics_methods.R (line 378, column 5)
cat() in R/seqpac_generics_methods.R (line 379, column 5)
cat() in R/seqpac_generics_methods.R (line 382, column 5)
cat() in R/seqpac_generics_methods.R (line 383, column 5)
cat() in R/seqpac_S4classes.R (line 357, column 12)
cat() in R/seqpac_S4classes.R (line 362, column 12)
cat() in R/simplify_reanno.R (line 229, column 5)
cat() in R/simplify_reanno.R (line 252, column 3)
print() in R/simplify_reanno.R (line 266, column 3)
cat() in R/tRNA_class.R (line 191, column 5)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/make_counts.R (line 294, column 15)
R/make_counts.R (line 530, column 13)
R/PAC_mapper.R (line 362, column 18)
R/PAC_mapper.R (line 363, column 20)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
suppressWarnings() in R/make_counts.R (line 221, column 7)
suppressWarnings() in R/PAC_filter.R (line 260, column 7)
suppressWarnings() in R/PAC_gtf.R (line 247, column 13)
suppressWarnings() in R/PAC_gtf.R (line 404, column 17)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 32 functions > 50 lines.
The longest 5 functions are:
make_trim() (R/make_trim.R, line 206): 530 lines
make_counts() (R/make_counts.R, line 188): 404 lines
PAC_trna() (R/PAC_trna.R, line 215): 377 lines
PAC_gtf() (R/PAC_gtf.R, line 125): 372 lines
add_reanno() (R/add_reanno.R, line 234): 279 lines
* Checking man page documentation...
* 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 multiples of 4 spaces for line indents, 4792
lines(25%) are not.
First 6 lines:
R/add_reanno.R:235 bio_perfect=FALSE, genome_max...
R/add_reanno.R:237 if(isS4(reanno)){
R/add_reanno.R:240 }else{
R/add_reanno.R:242 }
R/add_reanno.R:244 ## General setup ###############################
R/add_reanno.R:245 stopifnot(any(do.call("c", lapply(reanno$Full_anno...
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: 1
NOTE count: 7
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
===============================
BiocCheckGitClone('seqpac')
===============================
This is BiocCheckGitClone version 1.31.30. 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...
* Checking that provided CITATION file is correctly formatted...
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
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2275/0138aa29d65f0b5597adfb6067879d87dae7ec89/seqpac.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.4’
* 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 ‘seqpac’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 3.0Mb
* 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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [567s/464s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PAC_gtf 103.316 4.591 64.735
make_counts 64.492 3.298 60.743
add_reanno 24.126 6.326 23.637
make_reanno 23.915 6.493 23.433
map_reanno 24.149 6.233 23.541
PAC_deseq 28.415 0.459 28.888
make_pheno 24.003 2.852 19.402
make_PAC 23.096 2.918 19.270
make_cutadapt 20.420 0.092 20.512
make_trim 19.571 0.427 20.000
PAC_covplot 15.378 0.504 15.880
PAC_mapper 14.746 0.437 15.187
tRNA_class 5.574 5.305 7.615
PAC_trna 5.513 5.125 7.369
reanno 8.061 2.070 8.845
simplify_reanno 7.985 1.810 8.549
as.reanno 7.137 1.990 7.861
names 6.919 2.147 7.795
overview 6.833 1.840 7.405
full 6.536 2.008 7.318
map_rangetype 2.652 5.022 4.377
PAC_pca 5.290 0.064 5.355
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [541s/302s]
[541s/302s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
"", log_lst[[2]][log_rm_q]), out_quality = gsub("Output: | reads.",
"", log_lst[[2]][log_out_q]), stringsAsFactors = FALSE)
df[1, ] <- gsub("\\(", " \\(", as.character(unlist(df[1,
])))
df[1, ] <- gsub(" ", " ", as.character(unlist(df[1, ])))
if (!is.null(parse[[1]])) {
file.remove(temp_out)
}
return(df)
}`: task 1 failed - "error in running command"
Backtrace:
▆
1. ├─seqpac quiet(...) at test_PAC_generation.R:61:4
2. │ └─base::force(x) at test_PAC_generation.R:12:4
3. └─seqpac::make_counts(...)
4. └─seqpac::make_cutadapt(...)
5. └─... %dopar% ...
6. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
Error: Test failures
Execution halted
* 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 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2275/0138aa29d65f0b5597adfb6067879d87dae7ec89/seqpac.Rcheck/00check.log’
for details.
===============================
BiocCheck('seqpac_0.99.4.tar.gz')
===============================
This is BiocCheck version 1.31.30. 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 '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2275/0138aa29d65f0b5597adfb6067879d87dae7ec89/seqpac_0.99.4.tar.gz" "/tmp/RtmpFYMXUQ/file30cf2037a4beed/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...
* 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...
Workflow
* 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...
* WARNING: Import mcols, as, new, setMethod, terms.formula in
DESCRIPTION as well as NAMESPACE.
* 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 seqpac...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
add_reanno.R (line 264, column 15)
add_reanno.R (line 269, column 17)
add_reanno.R (line 319, column 16)
add_reanno.R (line 343, column 17)
add_reanno.R (line 464, column 49)
add_reanno.R (line 468, column 55)
filtsep_bin.R (line 68, column 12)
import_reanno.R (line 137, column 13)
import_reanno.R (line 201, column 51)
make_conv.R (line 157, column 12)
make_conv.R (line 192, column 14)
make_conv.R (line 229, column 12)
make_conv.R (line 291, column 14)
make_counts.R (line 369, column 35)
make_counts.R (line 455, column 35)
make_counts.R (line 522, column 40)
make_cutadapt.R (line 172, column 37)
make_pheno.R (line 199, column 16)
make_pheno.R (line 206, column 16)
make_reanno.R (line 230, column 16)
make_reanno.R (line 232, column 12)
make_reanno.R (line 283, column 14)
make_reanno.R (line 288, column 18)
make_reanno.R (line 315, column 15)
make_trim.R (line 242, column 42)
make_trim.R (line 300, column 7)
make_trim.R (line 409, column 18)
make_trim.R (line 619, column 53)
make_trim.R (line 649, column 14)
make_trim.R (line 662, column 12)
map_rangetype.R (line 129, column 48)
map_rangetype.R (line 152, column 14)
map_rangetype.R (line 225, column 17)
map_rangetype.R (line 312, column 14)
map_rangetype.R (line 377, column 17)
map_rangetype.R (line 383, column 17)
map_reanno.R (line 361, column 12)
map_reanno.R (line 371, column 15)
merge_lanes.R (line 142, column 30)
merge_lanes.R (line 150, column 14)
PAC_check.R (line 118, column 52)
PAC_check.R (line 127, column 54)
PAC_covplot.R (line 219, column 14)
PAC_covplot.R (line 238, column 14)
PAC_covplot.R (line 262, column 12)
PAC_covplot.R (line 268, column 36)
PAC_covplot.R (line 272, column 30)
PAC_covplot.R (line 280, column 54)
PAC_covplot.R (line 301, column 12)
PAC_deseq.R (line 131, column 13)
PAC_filter.R (line 253, column 17)
PAC_gtf.R (line 142, column 21)
PAC_gtf.R (line 160, column 13)
PAC_gtf.R (line 279, column 12)
PAC_gtf.R (line 304, column 12)
PAC_gtf.R (line 355, column 36)
PAC_gtf.R (line 386, column 12)
PAC_gtf.R (line 392, column 39)
PAC_gtf.R (line 437, column 14)
PAC_gtf.R (line 441, column 16)
PAC_gtf.R (line 453, column 14)
PAC_gtf.R (line 457, column 16)
PAC_jitter.R (line 167, column 22)
PAC_mapper.R (line 260, column 12)
PAC_mapper.R (line 320, column 12)
PAC_mapper.R (line 358, column 49)
PAC_nbias.R (line 186, column 12)
PAC_norm.R (line 61, column 15)
PAC_pca.R (line 129, column 47)
PAC_pie.R (line 167, column 15)
PAC_pie.R (line 181, column 13)
PAC_pie.R (line 193, column 24)
PAC_pie.R (line 193, column 40)
PAC_saturation.R (line 86, column 41)
PAC_saturation.R (line 102, column 14)
PAC_saturation.R (line 188, column 35)
PAC_sizedist.R (line 174, column 14)
PAC_sizedist.R (line 197, column 12)
PAC_stackbar.R (line 153, column 15)
PAC_stackbar.R (line 167, column 13)
PAC_summary.R (line 144, column 50)
PAC_trna.R (line 339, column 23)
PAC_trna.R (line 359, column 16)
simplify_reanno.R (line 202, column 23)
simplify_reanno.R (line 264, column 15)
simplify_reanno.R (line 282, column 12)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/add_reanno.R (line 250, column 3)
cat() in R/add_reanno.R (line 253, column 5)
cat() in R/add_reanno.R (line 261, column 5)
cat() in R/add_reanno.R (line 281, column 9)
cat() in R/add_reanno.R (line 313, column 5)
cat() in R/add_reanno.R (line 333, column 5)
cat() in R/add_reanno.R (line 386, column 13)
cat() in R/add_reanno.R (line 425, column 9)
cat() in R/add_reanno.R (line 436, column 5)
cat() in R/add_reanno.R (line 485, column 5)
cat() in R/import_reanno.R (line 130, column 3)
cat() in R/import_reanno.R (line 138, column 5)
cat() in R/import_reanno.R (line 178, column 9)
cat() in R/import_reanno.R (line 186, column 9)
cat() in R/import_reanno.R (line 245, column 5)
cat() in R/make_conv.R (line 121, column 3)
cat() in R/make_conv.R (line 132, column 3)
cat() in R/make_conv.R (line 143, column 7)
cat() in R/make_conv.R (line 155, column 3)
cat() in R/make_conv.R (line 190, column 5)
cat() in R/make_conv.R (line 225, column 3)
cat() in R/make_conv.R (line 305, column 3)
cat() in R/make_counts.R (line 195, column 3)
cat() in R/make_counts.R (line 208, column 5)
cat() in R/make_counts.R (line 210, column 5)
cat() in R/make_counts.R (line 212, column 3)
cat() in R/make_counts.R (line 231, column 5)
cat() in R/make_counts.R (line 232, column 5)
cat() in R/make_counts.R (line 233, column 5)
cat() in R/make_counts.R (line 234, column 5)
cat() in R/make_counts.R (line 251, column 7)
cat() in R/make_counts.R (line 252, column 7)
cat() in R/make_counts.R (line 253, column 7)
cat() in R/make_counts.R (line 255, column 7)
cat() in R/make_counts.R (line 256, column 7)
cat() in R/make_counts.R (line 258, column 7)
cat() in R/make_counts.R (line 280, column 5)
cat() in R/make_counts.R (line 281, column 5)
cat() in R/make_counts.R (line 282, column 5)
cat() in R/make_counts.R (line 283, column 5)
cat() in R/make_counts.R (line 302, column 7)
cat() in R/make_counts.R (line 303, column 7)
cat() in R/make_counts.R (line 304, column 7)
cat() in R/make_counts.R (line 305, column 7)
cat() in R/make_counts.R (line 307, column 7)
cat() in R/make_counts.R (line 308, column 7)
cat() in R/make_counts.R (line 310, column 7)
cat() in R/make_counts.R (line 311, column 7)
cat() in R/make_counts.R (line 313, column 7)
cat() in R/make_counts.R (line 314, column 7)
cat() in R/make_counts.R (line 316, column 7)
cat() in R/make_counts.R (line 353, column 3)
cat() in R/make_counts.R (line 390, column 3)
cat() in R/make_counts.R (line 422, column 5)
cat() in R/make_counts.R (line 439, column 5)
cat() in R/make_counts.R (line 443, column 7)
cat() in R/make_counts.R (line 445, column 7)
cat() in R/make_counts.R (line 482, column 3)
print() in R/make_counts.R (line 213, column 3)
print() in R/make_counts.R (line 254, column 7)
print() in R/make_counts.R (line 257, column 7)
print() in R/make_counts.R (line 306, column 7)
print() in R/make_counts.R (line 309, column 7)
print() in R/make_counts.R (line 312, column 7)
print() in R/make_counts.R (line 315, column 7)
print() in R/make_counts.R (line 580, column 5)
cat() in R/make_cutadapt.R (line 135, column 3)
cat() in R/make_cutadapt.R (line 136, column 3)
cat() in R/make_pheno.R (line 221, column 5)
cat() in R/make_pheno.R (line 226, column 7)
cat() in R/make_pheno.R (line 228, column 5)
cat() in R/make_pheno.R (line 236, column 5)
cat() in R/make_pheno.R (line 256, column 5)
cat() in R/make_pheno.R (line 261, column 3)
print() in R/make_pheno.R (line 229, column 5)
cat() in R/make_reanno.R (line 243, column 3)
cat() in R/make_reanno.R (line 301, column 3)
cat() in R/make_reanno.R (line 334, column 5)
cat() in R/make_reanno.R (line 354, column 7)
cat() in R/make_reanno.R (line 358, column 7)
cat() in R/make_reanno.R (line 360, column 7)
cat() in R/make_reanno.R (line 368, column 7)
cat() in R/make_trim.R (line 225, column 5)
cat() in R/make_trim.R (line 230, column 7)
cat() in R/make_trim.R (line 234, column 5)
cat() in R/make_trim.R (line 244, column 5)
cat() in R/make_trim.R (line 260, column 5)
cat() in R/make_trim.R (line 295, column 3)
cat() in R/make_trim.R (line 296, column 3)
cat() in R/map_rangetype.R (line 271, column 7)
cat() in R/map_rangetype.R (line 286, column 7)
cat() in R/map_rangetype.R (line 292, column 7)
print() in R/map_rangetype.R (line 294, column 7)
cat() in R/map_reanno.R (line 308, column 7)
cat() in R/map_reanno.R (line 345, column 5)
cat() in R/map_reanno.R (line 346, column 5)
cat() in R/map_reanno.R (line 347, column 5)
cat() in R/map_reanno.R (line 348, column 5)
cat() in R/map_reanno.R (line 355, column 5)
cat() in R/map_reanno.R (line 356, column 5)
cat() in R/map_reanno.R (line 357, column 5)
cat() in R/map_reanno.R (line 362, column 5)
cat() in R/map_reanno.R (line 363, column 5)
cat() in R/map_reanno.R (line 365, column 5)
cat() in R/map_reanno.R (line 372, column 7)
cat() in R/map_reanno.R (line 382, column 9)
cat() in R/map_reanno.R (line 395, column 9)
cat() in R/map_reanno.R (line 430, column 25)
cat() in R/map_reanno.R (line 433, column 11)
cat() in R/map_reanno.R (line 434, column 5)
cat() in R/map_reanno.R (line 436, column 3)
cat() in R/map_reanno.R (line 437, column 3)
cat() in R/map_reanno.R (line 442, column 3)
cat() in R/map_reanno.R (line 443, column 3)
cat() in R/PAC_covplot.R (line 196, column 3)
cat() in R/PAC_covplot.R (line 201, column 3)
cat() in R/PAC_covplot.R (line 204, column 7)
cat() in R/PAC_covplot.R (line 207, column 7)
print() in R/PAC_covplot.R (line 208, column 7)
print() in R/PAC_covplot.R (line 227, column 5)
cat() in R/PAC_deseq.R (line 118, column 3)
cat() in R/PAC_deseq.R (line 167, column 3)
cat() in R/PAC_deseq.R (line 168, column 3)
cat() in R/PAC_deseq.R (line 169, column 3)
cat() in R/PAC_deseq.R (line 170, column 3)
cat() in R/PAC_deseq.R (line 173, column 15)
cat() in R/PAC_deseq.R (line 176, column 5)
print() in R/PAC_deseq.R (line 178, column 5)
print() in R/PAC_deseq.R (line 233, column 3)
cat() in R/PAC_filter.R (line 133, column 7)
cat() in R/PAC_filter.R (line 178, column 7)
cat() in R/PAC_filter.R (line 206, column 7)
cat() in R/PAC_filter.R (line 219, column 7)
cat() in R/PAC_filter.R (line 222, column 7)
cat() in R/PAC_filter.R (line 288, column 7)
cat() in R/PAC_filter.R (line 300, column 7)
print() in R/PAC_filter.R (line 286, column 7)
cat() in R/PAC_gtf.R (line 145, column 3)
cat() in R/PAC_gtf.R (line 195, column 7)
cat() in R/PAC_gtf.R (line 202, column 9)
cat() in R/PAC_gtf.R (line 274, column 3)
cat() in R/PAC_gtf.R (line 299, column 3)
cat() in R/PAC_gtf.R (line 315, column 7)
cat() in R/PAC_gtf.R (line 326, column 7)
cat() in R/PAC_gtf.R (line 327, column 7)
cat() in R/PAC_gtf.R (line 337, column 3)
cat() in R/PAC_gtf.R (line 388, column 5)
cat() in R/PAC_gtf.R (line 434, column 5)
cat() in R/PAC_gtf.R (line 438, column 7)
cat() in R/PAC_gtf.R (line 450, column 5)
cat() in R/PAC_gtf.R (line 454, column 7)
cat() in R/PAC_mapper.R (line 168, column 5)
cat() in R/PAC_mapper.R (line 172, column 7)
cat() in R/PAC_mapper.R (line 176, column 9)
cat() in R/PAC_mapper.R (line 222, column 5)
cat() in R/PAC_mapper.R (line 228, column 7)
cat() in R/PAC_mapper.R (line 229, column 7)
print() in R/PAC_mapper.R (line 279, column 9)
print() in R/PAC_mapper.R (line 288, column 9)
cat() in R/PAC_nbias.R (line 149, column 4)
print() in R/PAC_pca.R (line 221, column 3)
print() in R/PAC_pie.R (line 256, column 5)
cat() in R/PAC_saturation.R (line 71, column 3)
cat() in R/PAC_saturation.R (line 80, column 3)
cat() in R/PAC_saturation.R (line 82, column 3)
cat() in R/PAC_saturation.R (line 84, column 3)
cat() in R/PAC_saturation.R (line 122, column 3)
cat() in R/PAC_trna.R (line 443, column 12)
cat() in R/seqpac_generics_methods.R (line 366, column 3)
cat() in R/seqpac_generics_methods.R (line 367, column 3)
cat() in R/seqpac_generics_methods.R (line 368, column 3)
cat() in R/seqpac_generics_methods.R (line 374, column 3)
cat() in R/seqpac_generics_methods.R (line 375, column 3)
cat() in R/seqpac_generics_methods.R (line 376, column 3)
cat() in R/seqpac_generics_methods.R (line 378, column 5)
cat() in R/seqpac_generics_methods.R (line 379, column 5)
cat() in R/seqpac_generics_methods.R (line 382, column 5)
cat() in R/seqpac_generics_methods.R (line 383, column 5)
cat() in R/seqpac_S4classes.R (line 357, column 12)
cat() in R/seqpac_S4classes.R (line 362, column 12)
cat() in R/simplify_reanno.R (line 229, column 5)
cat() in R/simplify_reanno.R (line 252, column 3)
print() in R/simplify_reanno.R (line 266, column 3)
cat() in R/tRNA_class.R (line 191, column 5)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/make_counts.R (line 294, column 15)
R/make_counts.R (line 530, column 13)
R/PAC_mapper.R (line 362, column 18)
R/PAC_mapper.R (line 363, column 20)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
suppressWarnings() in R/make_counts.R (line 221, column 7)
suppressWarnings() in R/PAC_filter.R (line 260, column 7)
suppressWarnings() in R/PAC_gtf.R (line 247, column 13)
suppressWarnings() in R/PAC_gtf.R (line 404, column 17)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 32 functions > 50 lines.
The longest 5 functions are:
make_trim() (R/make_trim.R, line 206): 530 lines
make_counts() (R/make_counts.R, line 188): 404 lines
PAC_trna() (R/PAC_trna.R, line 215): 377 lines
PAC_gtf() (R/PAC_gtf.R, line 125): 372 lines
add_reanno() (R/add_reanno.R, line 234): 279 lines
* Checking man page documentation...
* 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 multiples of 4 spaces for line indents, 4792
lines(25%) are not.
First 6 lines:
R/add_reanno.R:235 bio_perfect=FALSE, genome_max...
R/add_reanno.R:237 if(isS4(reanno)){
R/add_reanno.R:240 }else{
R/add_reanno.R:242 }
R/add_reanno.R:244 ## General setup ###############################
R/add_reanno.R:245 stopifnot(any(do.call("c", lapply(reanno$Full_anno...
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: 1
NOTE count: 7
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