merida1 Summary
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| Package: seqpac |
| Version: 0.99.2 |
| 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 19.03 seconds |
| CheckCommand: BiocCheckGitClone('seqpac') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqpac_0.99.2.tar.gz && BiocCheck('seqpac_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 12 minutes 31.87 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh seqpac_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 10.42 seconds |
| PackageFileSize: 5785.36 KiB |
| BuildID:: seqpac_20211214165310 |
| 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: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
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_0.99.2.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('seqpac')
===============================
This is BiocCheckGitClone version 1.31.15. 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...
* NOTE: CITATION file might be not correctly formatted
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 1
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/2275/8b6237424ffed57a45546103351cb68a434b570d/seqpac.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘0.99.2’
* 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 serialization versions ... OK
* checking whether package ‘seqpac’ can be installed ... [8s/8s] OK
* checking installed package size ... NOTE
installed size is 29.9Mb
sub-directories of 1Mb or more:
extdata 28.4Mb
* 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 ... [13s/13s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13m/11m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_counts 164.557 3.128 167.686
PAC_gtf 162.486 3.694 99.975
make_trim 77.882 1.069 78.946
make_PAC 43.188 1.009 44.196
make_pheno 42.059 0.788 42.847
make_cutadapt 40.101 0.471 40.571
PAC_covplot 22.944 0.413 23.369
PAC_mapper 20.676 0.294 20.988
make_reanno 13.161 1.729 13.342
map_reanno 13.095 1.726 13.295
add_reanno 12.862 1.640 13.004
simplify_reanno 11.596 1.700 11.775
reanno 11.192 1.693 11.359
as.reanno 10.274 1.662 10.423
names 8.963 1.706 9.130
overview 8.771 1.625 8.883
full 8.429 1.595 8.507
PAC_pca 7.039 0.130 7.183
PAC_jitter 6.232 0.140 6.387
PAC_nbias 6.320 0.024 6.353
* 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 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2275/8b6237424ffed57a45546103351cb68a434b570d/seqpac.Rcheck/00check.log’
for details.
===============================
BiocCheck('seqpac_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.15. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* 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...
Workflow
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
BasicWorkflow
See http://bioconductor.org/developers/how-to/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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: Potential intermediate files found:
vignettes/seqpac_-_a_guide_to_srna_analysis_using_sequence-based_counts.html
* 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 246, column 15)
add_reanno.R (line 251, column 17)
add_reanno.R (line 301, column 16)
add_reanno.R (line 318, column 15)
add_reanno.R (line 324, column 17)
add_reanno.R (line 445, column 49)
add_reanno.R (line 449, column 55)
filtsep_bin.R (line 70, column 15)
import_reanno.R (line 107, column 13)
import_reanno.R (line 171, column 51)
make_conv.R (line 154, column 12)
make_conv.R (line 189, column 14)
make_conv.R (line 226, column 12)
make_conv.R (line 290, column 14)
make_conv.R (line 292, column 40)
make_counts.R (line 401, column 35)
make_counts.R (line 487, column 35)
make_counts.R (line 552, column 40)
make_cutadapt.R (line 178, column 37)
make_pheno.R (line 207, column 16)
make_pheno.R (line 214, column 16)
make_reanno.R (line 209, column 16)
make_reanno.R (line 211, column 12)
make_reanno.R (line 263, column 14)
make_reanno.R (line 268, column 18)
make_reanno.R (line 295, column 15)
make_trim.R (line 248, column 42)
make_trim.R (line 305, column 7)
make_trim.R (line 414, column 18)
make_trim.R (line 623, column 53)
make_trim.R (line 653, column 14)
make_trim.R (line 666, column 12)
map_rangetype.R (line 193, column 48)
map_rangetype.R (line 216, column 14)
map_rangetype.R (line 289, column 17)
map_rangetype.R (line 376, column 14)
map_rangetype.R (line 441, column 17)
map_rangetype.R (line 447, column 17)
map_reanno.R (line 342, column 12)
map_reanno.R (line 349, column 15)
merge_lanes.R (line 142, column 30)
merge_lanes.R (line 149, column 14)
PAC_check.R (line 116, column 52)
PAC_check.R (line 125, column 54)
PAC_covplot.R (line 232, column 14)
PAC_covplot.R (line 251, column 14)
PAC_covplot.R (line 275, column 12)
PAC_covplot.R (line 281, column 36)
PAC_covplot.R (line 285, column 30)
PAC_covplot.R (line 293, column 54)
PAC_covplot.R (line 314, column 12)
PAC_deseq.R (line 133, column 13)
PAC_filter.R (line 252, column 17)
PAC_gtf.R (line 265, column 21)
PAC_gtf.R (line 283, column 13)
PAC_gtf.R (line 402, column 12)
PAC_gtf.R (line 427, column 12)
PAC_gtf.R (line 478, column 36)
PAC_gtf.R (line 509, column 12)
PAC_gtf.R (line 515, column 39)
PAC_gtf.R (line 557, column 14)
PAC_gtf.R (line 561, column 16)
PAC_gtf.R (line 573, column 14)
PAC_gtf.R (line 577, column 16)
PAC_jitter.R (line 167, column 22)
PAC_mapper.R (line 309, column 12)
PAC_mapper.R (line 369, column 12)
PAC_mapper.R (line 407, column 49)
PAC_nbias.R (line 184, column 12)
PAC_norm.R (line 61, column 15)
PAC_pca.R (line 124, column 47)
PAC_pie.R (line 166, column 15)
PAC_pie.R (line 180, column 13)
PAC_pie.R (line 192, column 24)
PAC_pie.R (line 192, column 40)
PAC_saturation.R (line 81, column 41)
PAC_saturation.R (line 95, column 14)
PAC_saturation.R (line 159, column 35)
PAC_sizedist.R (line 173, column 14)
PAC_sizedist.R (line 196, column 12)
PAC_stackbar.R (line 152, column 15)
PAC_stackbar.R (line 166, column 13)
PAC_summary.R (line 144, column 50)
PAC_trna.R (line 312, column 23)
PAC_trna.R (line 332, column 16)
simplify_reanno.R (line 301, column 23)
simplify_reanno.R (line 363, column 15)
simplify_reanno.R (line 381, column 12)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/make_cutadapt.R (line 165, column 10)
R/make_reanno.R (line 321, column 12)
R/make_reanno.R (line 343, column 15)
R/make_trim.R (line 278, column 10)
R/map_reanno.R (line 293, column 15)
R/map_reanno.R (line 299, column 17)
R/map_reanno.R (line 305, column 14)
R/PAC_check.R (line 58, column 10)
R/PAC_check.R (line 62, column 10)
R/PAC_check.R (line 98, column 16)
R/PAC_check.R (line 104, column 16)
R/PAC_check.R (line 120, column 22)
R/PAC_check.R (line 129, column 24)
R/PAC_check.R (line 148, column 17)
R/PAC_check.R (line 168, column 11)
R/PAC_check.R (line 183, column 17)
R/PAC_check.R (line 192, column 20)
R/PAC_gtf.R (line 345, column 15)
R/PAC_summary.R (line 107, column 12)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/PAC_filter.R (line 114, column 11)
R/PAC_filter.R (line 227, column 12)
R/PAC_filter.R (line 230, column 12)
R/PAC_gtf.R (line 389, column 5)
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/add_reanno.Rd
Found @ in man/as.PAC.Rd
Found @ in man/as.reanno.Rd
Found @ in man/make_reanno.Rd
Found @ in man/map_reanno.Rd
Found @ in man/PAC.Rd
Found @ in man/reanno.Rd
Found @ in
vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 13
times)
suppressWarnings() in R/make_conv.R (line 293, column 7)
suppressWarnings() in R/make_counts.R (line 253, column 7)
suppressWarnings() in R/make_cutadapt.R (line 153, column 5)
suppressWarnings() in R/make_trim.R (line 285, column 5)
suppressWarnings() in R/map_reanno.R (line 309, column 5)
suppressWarnings() in R/PAC_filter.R (line 259, column 7)
suppressWarnings() in R/PAC_gtf.R (line 370, column 13)
suppressWarnings() in R/PAC_gtf.R (line 527, column 17)
suppressWarnings() in R/PAC_mapper.R (line 253, column 3)
suppressWarnings() in R/PAC_mapper.R (line 257, column 3)
suppressMessages() in R/PAC_pca.R (line 105, column 12)
suppressMessages() in R/PAC_pca.R (line 109, column 12)
suppressWarnings() in R/PAC_trna.R (line 466, column 9)
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 31 functions > 50 lines.
The longest 5 functions are:
make_trim() (R/make_trim.R, line 212): 526 lines
make_counts() (R/make_counts.R, line 221): 401 lines
PAC_gtf() (R/PAC_gtf.R, line 248): 369 lines
PAC_trna() (R/PAC_trna.R, line 188): 366 lines
add_reanno() (R/add_reanno.R, line 216): 278 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
import_reanno.Rd, map_rangetype.Rd, PAC_deseq.Rd, PAC_trna.Rd,
tRNA_class.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
18% of man pages use one of these cases.
Found in the following files:
import_reanno.Rd
make_conv.Rd
make_cutadapt.Rd
map_rangetype.Rd
PAC_deseq.Rd
PAC_gtf.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
import_reanno.Rd
make_conv.Rd
make_cutadapt.Rd
map_rangetype.Rd
PAC_deseq.Rd
PAC_gtf.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 224 lines (1%) are > 80 characters
long.
First 6 lines:
R/add_reanno.R:93 #' # Here we use the R temporary folder depending on ...
R/add_reanno.R:103 #' ## Then map your PAC-object against the fasta re...
R/add_reanno.R:108 #' ## Then import and generate a reanno-object of t...
R/add_reanno.R:109 #' reanno_biotype <- make_reanno(output, PAC=pac, mi...
R/filtsep_bin.R:39 #' pac_filt <- PAC_filter(pac, subset_only = TRUE, ...
R/filtsep_bin.R:66 df <- as.data.frame(matrix(NA, nrow=length(seqs...
* NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
tabs.
First 5 lines:
R/PAC_covplot.R:369 plot_lst[[i]] <- ggplot2::ggplot(cov_df, g...
R/PAC_filter.R:267 ggplot2::ggtitle("User filter:")+
R/PAC_filter.R:285 ### Promt for user input
R/PAC_gtf.R:110 #' pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
man/PAC_gtf.Rd:124 pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
* NOTE: Consider multiples of 4 spaces for line indents, 4835
lines(24%) are not.
First 6 lines:
R/add_reanno.R:217 bio_perfect=FALSE, genome_max...
R/add_reanno.R:218
R/add_reanno.R:219 if(isS4(reanno)){
R/add_reanno.R:222 }else{
R/add_reanno.R:224 }
R/add_reanno.R:225
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 16
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
BiocCheck FAILED.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir seqpac_0.99.2.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)
nebbiolo1 Summary
[top]
| Package: seqpac |
| Version: 0.99.2 |
| 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 34.90 seconds |
| CheckCommand: BiocCheckGitClone('seqpac') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings seqpac_0.99.2.tar.gz && BiocCheck('seqpac_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 15.01 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 5794.50 KiB |
| BuildID:: seqpac_20211214165310 |
| 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: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
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_0.99.2.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('seqpac')
===============================
This is BiocCheckGitClone version 1.31.15. 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...
* NOTE: CITATION file might be not correctly formatted
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 1
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/2275/8b6237424ffed57a45546103351cb68a434b570d/seqpac.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘0.99.2’
* 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 serialization versions ... OK
* checking whether package ‘seqpac’ can be installed ... [5s/5s] OK
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
extdata 6.9Mb
* 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 ... [8s/8s] 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 ... [631s/577s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_counts 154.349 0.536 154.891
PAC_gtf 103.706 4.204 64.970
make_trim 74.358 0.627 74.988
make_PAC 40.355 0.348 40.704
make_pheno 39.300 0.144 39.445
make_cutadapt 38.998 0.185 39.185
PAC_covplot 15.849 0.280 16.127
PAC_mapper 14.244 0.161 14.409
make_reanno 9.159 1.901 9.813
map_reanno 8.740 1.646 9.138
add_reanno 8.574 1.743 9.099
reanno 8.214 2.087 9.057
simplify_reanno 8.142 1.935 8.825
as.reanno 7.452 1.811 8.052
overview 7.053 2.011 7.806
names 7.061 1.890 7.695
full 6.697 1.842 7.334
PAC_pca 4.995 0.024 5.019
* 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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2275/8b6237424ffed57a45546103351cb68a434b570d/seqpac.Rcheck/00check.log’
for details.
===============================
BiocCheck('seqpac_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.15. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* 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...
Workflow
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
BasicWorkflow
See http://bioconductor.org/developers/how-to/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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: Potential intermediate files found:
vignettes/seqpac_-_a_guide_to_srna_analysis_using_sequence-based_counts.html
* 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 246, column 15)
add_reanno.R (line 251, column 17)
add_reanno.R (line 301, column 16)
add_reanno.R (line 318, column 15)
add_reanno.R (line 324, column 17)
add_reanno.R (line 445, column 49)
add_reanno.R (line 449, column 55)
filtsep_bin.R (line 70, column 15)
import_reanno.R (line 107, column 13)
import_reanno.R (line 171, column 51)
make_conv.R (line 154, column 12)
make_conv.R (line 189, column 14)
make_conv.R (line 226, column 12)
make_conv.R (line 290, column 14)
make_conv.R (line 292, column 40)
make_counts.R (line 401, column 35)
make_counts.R (line 487, column 35)
make_counts.R (line 552, column 40)
make_cutadapt.R (line 178, column 37)
make_pheno.R (line 207, column 16)
make_pheno.R (line 214, column 16)
make_reanno.R (line 209, column 16)
make_reanno.R (line 211, column 12)
make_reanno.R (line 263, column 14)
make_reanno.R (line 268, column 18)
make_reanno.R (line 295, column 15)
make_trim.R (line 248, column 42)
make_trim.R (line 305, column 7)
make_trim.R (line 414, column 18)
make_trim.R (line 623, column 53)
make_trim.R (line 653, column 14)
make_trim.R (line 666, column 12)
map_rangetype.R (line 193, column 48)
map_rangetype.R (line 216, column 14)
map_rangetype.R (line 289, column 17)
map_rangetype.R (line 376, column 14)
map_rangetype.R (line 441, column 17)
map_rangetype.R (line 447, column 17)
map_reanno.R (line 342, column 12)
map_reanno.R (line 349, column 15)
merge_lanes.R (line 142, column 30)
merge_lanes.R (line 149, column 14)
PAC_check.R (line 116, column 52)
PAC_check.R (line 125, column 54)
PAC_covplot.R (line 232, column 14)
PAC_covplot.R (line 251, column 14)
PAC_covplot.R (line 275, column 12)
PAC_covplot.R (line 281, column 36)
PAC_covplot.R (line 285, column 30)
PAC_covplot.R (line 293, column 54)
PAC_covplot.R (line 314, column 12)
PAC_deseq.R (line 133, column 13)
PAC_filter.R (line 252, column 17)
PAC_gtf.R (line 265, column 21)
PAC_gtf.R (line 283, column 13)
PAC_gtf.R (line 402, column 12)
PAC_gtf.R (line 427, column 12)
PAC_gtf.R (line 478, column 36)
PAC_gtf.R (line 509, column 12)
PAC_gtf.R (line 515, column 39)
PAC_gtf.R (line 557, column 14)
PAC_gtf.R (line 561, column 16)
PAC_gtf.R (line 573, column 14)
PAC_gtf.R (line 577, column 16)
PAC_jitter.R (line 167, column 22)
PAC_mapper.R (line 309, column 12)
PAC_mapper.R (line 369, column 12)
PAC_mapper.R (line 407, column 49)
PAC_nbias.R (line 184, column 12)
PAC_norm.R (line 61, column 15)
PAC_pca.R (line 124, column 47)
PAC_pie.R (line 166, column 15)
PAC_pie.R (line 180, column 13)
PAC_pie.R (line 192, column 24)
PAC_pie.R (line 192, column 40)
PAC_saturation.R (line 81, column 41)
PAC_saturation.R (line 95, column 14)
PAC_saturation.R (line 159, column 35)
PAC_sizedist.R (line 173, column 14)
PAC_sizedist.R (line 196, column 12)
PAC_stackbar.R (line 152, column 15)
PAC_stackbar.R (line 166, column 13)
PAC_summary.R (line 144, column 50)
PAC_trna.R (line 312, column 23)
PAC_trna.R (line 332, column 16)
simplify_reanno.R (line 301, column 23)
simplify_reanno.R (line 363, column 15)
simplify_reanno.R (line 381, column 12)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/make_cutadapt.R (line 165, column 10)
R/make_reanno.R (line 321, column 12)
R/make_reanno.R (line 343, column 15)
R/make_trim.R (line 278, column 10)
R/map_reanno.R (line 293, column 15)
R/map_reanno.R (line 299, column 17)
R/map_reanno.R (line 305, column 14)
R/PAC_check.R (line 58, column 10)
R/PAC_check.R (line 62, column 10)
R/PAC_check.R (line 98, column 16)
R/PAC_check.R (line 104, column 16)
R/PAC_check.R (line 120, column 22)
R/PAC_check.R (line 129, column 24)
R/PAC_check.R (line 148, column 17)
R/PAC_check.R (line 168, column 11)
R/PAC_check.R (line 183, column 17)
R/PAC_check.R (line 192, column 20)
R/PAC_gtf.R (line 345, column 15)
R/PAC_summary.R (line 107, column 12)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/PAC_filter.R (line 114, column 11)
R/PAC_filter.R (line 227, column 12)
R/PAC_filter.R (line 230, column 12)
R/PAC_gtf.R (line 389, column 5)
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/add_reanno.Rd
Found @ in man/as.PAC.Rd
Found @ in man/as.reanno.Rd
Found @ in man/make_reanno.Rd
Found @ in man/map_reanno.Rd
Found @ in man/PAC.Rd
Found @ in man/reanno.Rd
Found @ in
vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 13
times)
suppressWarnings() in R/make_conv.R (line 293, column 7)
suppressWarnings() in R/make_counts.R (line 253, column 7)
suppressWarnings() in R/make_cutadapt.R (line 153, column 5)
suppressWarnings() in R/make_trim.R (line 285, column 5)
suppressWarnings() in R/map_reanno.R (line 309, column 5)
suppressWarnings() in R/PAC_filter.R (line 259, column 7)
suppressWarnings() in R/PAC_gtf.R (line 370, column 13)
suppressWarnings() in R/PAC_gtf.R (line 527, column 17)
suppressWarnings() in R/PAC_mapper.R (line 253, column 3)
suppressWarnings() in R/PAC_mapper.R (line 257, column 3)
suppressMessages() in R/PAC_pca.R (line 105, column 12)
suppressMessages() in R/PAC_pca.R (line 109, column 12)
suppressWarnings() in R/PAC_trna.R (line 466, column 9)
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 31 functions > 50 lines.
The longest 5 functions are:
make_trim() (R/make_trim.R, line 212): 526 lines
make_counts() (R/make_counts.R, line 221): 401 lines
PAC_gtf() (R/PAC_gtf.R, line 248): 369 lines
PAC_trna() (R/PAC_trna.R, line 188): 366 lines
add_reanno() (R/add_reanno.R, line 216): 278 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
import_reanno.Rd, map_rangetype.Rd, PAC_deseq.Rd, PAC_trna.Rd,
tRNA_class.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
18% of man pages use one of these cases.
Found in the following files:
import_reanno.Rd
make_conv.Rd
make_cutadapt.Rd
map_rangetype.Rd
PAC_deseq.Rd
PAC_gtf.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
import_reanno.Rd
make_conv.Rd
make_cutadapt.Rd
map_rangetype.Rd
PAC_deseq.Rd
PAC_gtf.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 224 lines (1%) are > 80 characters
long.
First 6 lines:
R/add_reanno.R:93 #' # Here we use the R temporary folder depending on ...
R/add_reanno.R:103 #' ## Then map your PAC-object against the fasta re...
R/add_reanno.R:108 #' ## Then import and generate a reanno-object of t...
R/add_reanno.R:109 #' reanno_biotype <- make_reanno(output, PAC=pac, mi...
R/filtsep_bin.R:39 #' pac_filt <- PAC_filter(pac, subset_only = TRUE, ...
R/filtsep_bin.R:66 df <- as.data.frame(matrix(NA, nrow=length(seqs...
* NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
tabs.
First 5 lines:
R/PAC_covplot.R:369 plot_lst[[i]] <- ggplot2::ggplot(cov_df, g...
R/PAC_filter.R:267 ggplot2::ggtitle("User filter:")+
R/PAC_filter.R:285 ### Promt for user input
R/PAC_gtf.R:110 #' pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
man/PAC_gtf.Rd:124 pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
* NOTE: Consider multiples of 4 spaces for line indents, 4835
lines(24%) are not.
First 6 lines:
R/add_reanno.R:217 bio_perfect=FALSE, genome_max...
R/add_reanno.R:218
R/add_reanno.R:219 if(isS4(reanno)){
R/add_reanno.R:222 }else{
R/add_reanno.R:224 }
R/add_reanno.R:225
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 16
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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