nebbiolo1 Summary
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| Package: seqpac |
| Version: 0.99.3 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data seqpac |
| BuildTime: 1 minutes 42.24 seconds |
| CheckCommand: BiocCheckGitClone('seqpac') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings seqpac_0.99.3.tar.gz && BiocCheck('seqpac_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 15 minutes 0.00 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3763.76 KiB |
| BuildID:: seqpac_20220201173124 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seqpac. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Workflow. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: -9. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* preparing ‘seqpac’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘seqpac_0.99.3.tar.gz’
nebbiolo1 CHECK output
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===============================
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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2275/7ecb616d932c020e89b93e18970c832bb17d49b4/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 ‘0.99.3’
* 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 ... 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 ... [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 ... [12m/11m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_counts 151.529 0.384 151.914
PAC_gtf 103.098 3.628 63.391
make_trim 72.897 0.608 73.507
make_PAC 39.079 0.391 39.471
make_pheno 38.532 0.140 38.674
make_cutadapt 37.661 0.128 37.790
make_reanno 24.387 6.181 23.775
add_reanno 23.872 6.336 23.481
map_reanno 24.032 5.937 23.158
PAC_deseq 28.804 0.401 29.217
PAC_covplot 15.419 0.445 15.864
PAC_mapper 15.258 0.354 15.621
tRNA_class 5.616 4.972 7.533
PAC_trna 5.417 4.740 7.195
reanno 7.968 1.989 8.725
simplify_reanno 7.927 1.894 8.556
overview 7.452 1.969 8.163
names 7.043 2.154 7.975
as.reanno 7.106 1.972 7.847
full 6.714 1.947 7.443
map_rangetype 2.566 4.648 4.177
PAC_pca 5.288 0.064 5.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('seqpac_0.99.3.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/2275/7ecb616d932c020e89b93e18970c832bb17d49b4/seqpac_0.99.3.tar.gz" "/tmp/Rtmp3dcXAH/file1681336eba9e3/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 402, column 35)
make_counts.R (line 488, column 35)
make_counts.R (line 555, column 40)
make_cutadapt.R (line 173, column 37)
make_pheno.R (line 207, column 16)
make_pheno.R (line 214, 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 248, column 42)
make_trim.R (line 306, column 7)
make_trim.R (line 415, column 18)
make_trim.R (line 625, column 53)
make_trim.R (line 655, column 14)
make_trim.R (line 668, 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 228, column 3)
cat() in R/make_counts.R (line 241, column 5)
cat() in R/make_counts.R (line 243, column 5)
cat() in R/make_counts.R (line 245, column 3)
cat() in R/make_counts.R (line 264, column 5)
cat() in R/make_counts.R (line 265, column 5)
cat() in R/make_counts.R (line 266, column 5)
cat() in R/make_counts.R (line 267, column 5)
cat() in R/make_counts.R (line 284, column 7)
cat() in R/make_counts.R (line 285, column 7)
cat() in R/make_counts.R (line 286, column 7)
cat() in R/make_counts.R (line 288, column 7)
cat() in R/make_counts.R (line 289, column 7)
cat() in R/make_counts.R (line 291, column 7)
cat() in R/make_counts.R (line 313, column 5)
cat() in R/make_counts.R (line 314, column 5)
cat() in R/make_counts.R (line 315, column 5)
cat() in R/make_counts.R (line 316, column 5)
cat() in R/make_counts.R (line 335, column 7)
cat() in R/make_counts.R (line 336, column 7)
cat() in R/make_counts.R (line 337, column 7)
cat() in R/make_counts.R (line 338, column 7)
cat() in R/make_counts.R (line 340, column 7)
cat() in R/make_counts.R (line 341, column 7)
cat() in R/make_counts.R (line 343, column 7)
cat() in R/make_counts.R (line 344, column 7)
cat() in R/make_counts.R (line 346, column 7)
cat() in R/make_counts.R (line 347, column 7)
cat() in R/make_counts.R (line 349, column 7)
cat() in R/make_counts.R (line 386, column 3)
cat() in R/make_counts.R (line 423, column 3)
cat() in R/make_counts.R (line 455, column 5)
cat() in R/make_counts.R (line 472, column 5)
cat() in R/make_counts.R (line 476, column 7)
cat() in R/make_counts.R (line 478, column 7)
cat() in R/make_counts.R (line 515, column 3)
print() in R/make_counts.R (line 246, column 3)
print() in R/make_counts.R (line 287, column 7)
print() in R/make_counts.R (line 290, column 7)
print() in R/make_counts.R (line 339, column 7)
print() in R/make_counts.R (line 342, column 7)
print() in R/make_counts.R (line 345, column 7)
print() in R/make_counts.R (line 348, column 7)
print() in R/make_counts.R (line 613, column 5)
cat() in R/make_cutadapt.R (line 136, column 3)
cat() in R/make_cutadapt.R (line 137, column 3)
cat() in R/make_pheno.R (line 229, column 5)
cat() in R/make_pheno.R (line 234, column 7)
cat() in R/make_pheno.R (line 236, column 5)
cat() in R/make_pheno.R (line 244, column 5)
cat() in R/make_pheno.R (line 264, column 5)
cat() in R/make_pheno.R (line 269, column 3)
print() in R/make_pheno.R (line 237, 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 231, column 5)
cat() in R/make_trim.R (line 236, column 7)
cat() in R/make_trim.R (line 240, column 5)
cat() in R/make_trim.R (line 250, column 5)
cat() in R/make_trim.R (line 266, column 5)
cat() in R/make_trim.R (line 301, column 3)
cat() in R/make_trim.R (line 302, 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 327, column 15)
R/make_counts.R (line 563, 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 254, 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 212): 530 lines
make_counts() (R/make_counts.R, line 221): 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, 4829
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
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: seqpac |
| Version: 0.99.3 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data seqpac |
| BuildTime: 2 minutes 29.82 seconds |
| CheckCommand: BiocCheckGitClone('seqpac') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqpac_0.99.3.tar.gz && BiocCheck('seqpac_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.95 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh seqpac_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 11.62 seconds |
| PackageFileSize: 3744.01 KiB |
| BuildID:: seqpac_20220201173124 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seqpac. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Workflow. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: -9. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* preparing ‘seqpac’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘seqpac_0.99.3.tar.gz’
merida1 CHECK output
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===============================
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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2275/7ecb616d932c020e89b93e18970c832bb17d49b4/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 ‘0.99.3’
* 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/11s] 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 ... [15m/14m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_counts 166.154 3.150 169.304
PAC_gtf 160.060 3.031 97.045
make_trim 77.866 1.070 78.933
PAC_deseq 47.913 0.370 48.290
make_PAC 42.908 1.016 43.924
make_pheno 42.900 0.787 43.687
add_reanno 35.992 5.829 32.181
map_reanno 35.761 5.997 31.911
make_reanno 35.694 5.939 31.829
make_cutadapt 40.259 0.461 40.721
PAC_covplot 22.594 0.386 23.005
PAC_mapper 21.309 0.478 21.808
simplify_reanno 11.677 1.776 11.880
reanno 11.262 1.752 11.466
as.reanno 10.348 1.692 10.529
names 9.044 1.767 9.265
overview 8.875 1.726 9.039
tRNA_class 8.577 1.713 9.915
full 8.504 1.633 8.628
PAC_trna 8.446 1.629 9.699
PAC_pca 7.518 0.090 7.623
PAC_nbias 7.231 0.019 7.254
PAC_jitter 6.564 0.152 6.731
map_rangetype 3.962 1.516 5.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('seqpac_0.99.3.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/2275/7ecb616d932c020e89b93e18970c832bb17d49b4/seqpac_0.99.3.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmprUNdQ6/filed999189c8c79/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 402, column 35)
make_counts.R (line 488, column 35)
make_counts.R (line 555, column 40)
make_cutadapt.R (line 173, column 37)
make_pheno.R (line 207, column 16)
make_pheno.R (line 214, 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 248, column 42)
make_trim.R (line 306, column 7)
make_trim.R (line 415, column 18)
make_trim.R (line 625, column 53)
make_trim.R (line 655, column 14)
make_trim.R (line 668, 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 228, column 3)
cat() in R/make_counts.R (line 241, column 5)
cat() in R/make_counts.R (line 243, column 5)
cat() in R/make_counts.R (line 245, column 3)
cat() in R/make_counts.R (line 264, column 5)
cat() in R/make_counts.R (line 265, column 5)
cat() in R/make_counts.R (line 266, column 5)
cat() in R/make_counts.R (line 267, column 5)
cat() in R/make_counts.R (line 284, column 7)
cat() in R/make_counts.R (line 285, column 7)
cat() in R/make_counts.R (line 286, column 7)
cat() in R/make_counts.R (line 288, column 7)
cat() in R/make_counts.R (line 289, column 7)
cat() in R/make_counts.R (line 291, column 7)
cat() in R/make_counts.R (line 313, column 5)
cat() in R/make_counts.R (line 314, column 5)
cat() in R/make_counts.R (line 315, column 5)
cat() in R/make_counts.R (line 316, column 5)
cat() in R/make_counts.R (line 335, column 7)
cat() in R/make_counts.R (line 336, column 7)
cat() in R/make_counts.R (line 337, column 7)
cat() in R/make_counts.R (line 338, column 7)
cat() in R/make_counts.R (line 340, column 7)
cat() in R/make_counts.R (line 341, column 7)
cat() in R/make_counts.R (line 343, column 7)
cat() in R/make_counts.R (line 344, column 7)
cat() in R/make_counts.R (line 346, column 7)
cat() in R/make_counts.R (line 347, column 7)
cat() in R/make_counts.R (line 349, column 7)
cat() in R/make_counts.R (line 386, column 3)
cat() in R/make_counts.R (line 423, column 3)
cat() in R/make_counts.R (line 455, column 5)
cat() in R/make_counts.R (line 472, column 5)
cat() in R/make_counts.R (line 476, column 7)
cat() in R/make_counts.R (line 478, column 7)
cat() in R/make_counts.R (line 515, column 3)
print() in R/make_counts.R (line 246, column 3)
print() in R/make_counts.R (line 287, column 7)
print() in R/make_counts.R (line 290, column 7)
print() in R/make_counts.R (line 339, column 7)
print() in R/make_counts.R (line 342, column 7)
print() in R/make_counts.R (line 345, column 7)
print() in R/make_counts.R (line 348, column 7)
print() in R/make_counts.R (line 613, column 5)
cat() in R/make_cutadapt.R (line 136, column 3)
cat() in R/make_cutadapt.R (line 137, column 3)
cat() in R/make_pheno.R (line 229, column 5)
cat() in R/make_pheno.R (line 234, column 7)
cat() in R/make_pheno.R (line 236, column 5)
cat() in R/make_pheno.R (line 244, column 5)
cat() in R/make_pheno.R (line 264, column 5)
cat() in R/make_pheno.R (line 269, column 3)
print() in R/make_pheno.R (line 237, 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 231, column 5)
cat() in R/make_trim.R (line 236, column 7)
cat() in R/make_trim.R (line 240, column 5)
cat() in R/make_trim.R (line 250, column 5)
cat() in R/make_trim.R (line 266, column 5)
cat() in R/make_trim.R (line 301, column 3)
cat() in R/make_trim.R (line 302, 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 327, column 15)
R/make_counts.R (line 563, 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 254, 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 212): 530 lines
make_counts() (R/make_counts.R, line 221): 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, 4829
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
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir seqpac_0.99.3.tar.gz'
>>>>>>>
* installing *source* package ‘seqpac’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘norm’ in package ‘seqpac’
Creating a new generic function for ‘summary’ in package ‘seqpac’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘seqpac’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqpac)