===============================
BiocCheckGitClone('seqpac')
===============================
This is BiocCheckGitClone version 1.29.14. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
seqpac.Rproj
* 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: 1
WARNING count: 0
NOTE count: 1
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2275/seqpac_20210922162949/seqpac.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.0’
* 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 20.1Mb
sub-directories of 1Mb or more:
extdata 18.4Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
GLP-3 + file LICENSE
Standardizable: FALSE
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘seqpac’ for: ‘show’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
Namespaces in Imports field not imported from:
‘readr’ ‘tidyr’
All declared Imports should be used.
Missing or unexported object: ‘DESeq2::summary.DESeqResults’
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
‘anno<-’ ‘counts<-’ ‘full<-’ ‘norm<-’ ‘overview<-’ ‘pheno<-’
‘summary<-’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
PAC: no visible global function definition for ‘new’
PAC_check: no visible global function definition for ‘as’
PAC_covplot: no visible global function definition for ‘as’
PAC_deseq: no visible global function definition for ‘as’
PAC_filter: no visible global function definition for ‘as’
PAC_filtsep: no visible global function definition for ‘as’
PAC_gtf: no visible global function definition for ‘as’
PAC_jitter: no visible global function definition for ‘as’
PAC_mapper: no visible global function definition for ‘as’
PAC_nbias: no visible global function definition for ‘as’
PAC_norm: no visible global function definition for ‘as’
PAC_pca: no visible global function definition for ‘as’
PAC_pie: no visible global function definition for ‘as’
PAC_saturation: no visible global function definition for ‘as’
PAC_sizedist: no visible global function definition for ‘as’
PAC_stackbar: no visible global function definition for ‘as’
PAC_summary: no visible global function definition for ‘as’
PAC_trna: no visible global function definition for ‘as’
add_reanno: no visible global function definition for ‘as’
length.PAC: no visible global function definition for ‘as’
length.reanno: no visible global function definition for ‘as’
make_counts: no visible binding for global variable ‘i’
make_reanno: no visible global function definition for ‘as’
map_reanno: no visible global function definition for ‘as’
merge_lanes: no visible binding for global variable ‘j’
names.PAC: no visible global function definition for ‘as’
names.reanno: no visible global function definition for ‘as’
reanno: no visible global function definition for ‘new’
show.PAC: no visible global function definition for ‘as’
simplify_reanno: no visible global function definition for ‘as’
summary.PAC: no visible global function definition for ‘as’
length,PAC: no visible global function definition for ‘as’
length,reanno: no visible global function definition for ‘as’
names,PAC: no visible global function definition for ‘as’
names,reanno: no visible global function definition for ‘as’
show,PAC: no visible global function definition for ‘as’
summary,PAC: no visible global function definition for ‘as’
Undefined global functions or variables:
as i j new
Consider adding
importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'map_reanno.Rd':
‘[QuasR]{Rbowtie::bowtie_build}’ ‘[QuasR]{Rbowtie::bowtie}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'anno':
anno<-
Code: function(object)
Docs: function(object, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'counts':
counts<-
Code: function(object)
Docs: function(object, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'full':
full<-
Code: function(x)
Docs: function(x, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'norm':
norm<-
Code: function(object)
Docs: function(object, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'overview':
overview<-
Code: function(x)
Docs: function(x, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'pheno':
pheno<-
Code: function(object)
Docs: function(object, value)
Argument names in docs not in code:
value
Codoc mismatches from documentation object 'summary':
summary<-
Code: function(object)
Docs: function(object, value)
Argument names in docs not in code:
value
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'PAC-class'
‘Pheno’ ‘Anno’ ‘Counts’ ‘norm’ ‘summary’ ‘reanno’
Undocumented arguments in documentation object 'PAC_gtf'
‘target’
Documented arguments not in \usage in documentation object 'PAC_gtf':
‘targets’
Undocumented arguments in documentation object 'anno'
‘object’ ‘value’
Undocumented arguments in documentation object 'colnames,PAC-method'
‘x’
Undocumented arguments in documentation object 'counts'
‘object’ ‘value’
Undocumented arguments in documentation object 'full'
‘x’ ‘value’
Undocumented arguments in documentation object 'length,PAC-method'
‘x’
Undocumented arguments in documentation object 'names,PAC-method'
‘x’
Undocumented arguments in documentation object 'ncol,PAC-method'
‘x’
Undocumented arguments in documentation object 'norm'
‘object’ ‘value’
Undocumented arguments in documentation object 'nrow,PAC-method'
‘x’
Undocumented arguments in documentation object 'overview'
‘x’ ‘value’
Undocumented arguments in documentation object 'pheno'
‘object’ ‘value’
Undocumented arguments in documentation object 'reanno-class'
‘Overview’ ‘Full_anno’
Undocumented arguments in documentation object 'rownames,reanno-method'
‘x’
Undocumented arguments in documentation object 'show,PAC-method'
‘object’
Undocumented arguments in documentation object 'summary'
‘object’ ‘value’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [44s/44s] ERROR
Running examples in ‘seqpac-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.reanno
> ### Title: Converts an S3 reanno into a S4 reanno
> ### Aliases: as.reanno
>
> ### ** Examples
>
>
> library(seqpac)
>
> ## load data
> load(system.file("extdata", "drosophila_sRNA_pac_filt.Rdata",
+ package = "seqpac", mustWork = TRUE))
> pac = pac_cpm_filt
>
> ## Genome example
> # setup temporary output folder depending on windows or linux
>
> if(grepl("windows", .Platform$OS.type)){
+ output <- paste0(tempdir(), "\\seqpac\\test")
+ }else{
+ output <- paste0(tempdir(), "/seqpac/test")
+ }
>
> # Empty temp output folder
> out_fls <- list.files(output, recursive=TRUE, full.names = TRUE)
> suppressWarnings(file.remove(out_fls))
logical(0)
>
>
> # Run reanno workflow loading test genome fasta
> mycoplasma_path <- paste0(getwd(), "/tests/testthat/data_for_tests/mycoplasma_genome")
> ref_paths <- list(genome1= list.files(mycoplasma_path, pattern=".fa",
+ full.names = TRUE),
+ genome2= list.files(mycoplasma_path, pattern=".fa",
+ full.names = TRUE))
>
>
>
> map_reanno(PAC=pac, ref_paths=ref_paths, output_path=output,
+ type="internal", mismatches=3, import="genome",
+ threads=8, keep_temp=FALSE)
R internal mapping using the Rbowtie package was specified.
This package uses bowtie version 1.3.0.
If you need a newer version, please install Bowtie manually
outside R and then use option type='external'.
******************************************************
|--- Mismatch 0 started at 12:32:02
|--- Bowtie mapping:
|---> genome1...
Error in if (!is.character(index) || !file.exists(dirname(index))) stop("Argument 'index' has to be a character scalar giving the path to the index directory.") :
missing value where TRUE/FALSE needed
Calls: map_reanno -> eval -> eval -> <Anonymous>
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, 6 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2275/seqpac_20210922162949/seqpac.Rcheck/00check.log’
for details.
===============================
BiocCheck('seqpac_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.29.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 31 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
add_reanno (as)
length.PAC (as)
length.reanno (as)
make_counts (i)
make_reanno (as)
map_reanno (as)
merge_lanes (j)
names.PAC (as)
names.reanno (as)
PAC (new)
PAC_check (as)
PAC_covplot (as)
PAC_deseq (as)
PAC_filter (as)
PAC_filtsep (as)
PAC_gtf (as)
PAC_jitter (as)
PAC_mapper (as)
PAC_nbias (as)
PAC_norm (as)
PAC_pca (as)
PAC_pie (as)
PAC_saturation (as)
PAC_sizedist (as)
PAC_stackbar (as)
PAC_summary (as)
PAC_trna (as)
reanno (new)
show.PAC (as)
simplify_reanno (as)
summary.PAC (as)
* 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...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 19.7724 MB
Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* WARNING: 'Workflow EpigeneticWorkflow AnnotationWorkflow
GeneExpressionWorkflow' is an invalid BiocViews term.
* Checking for recommended biocViews...
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 'GLP-3 + file LICENSE' unknown; licenses cannot
restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import readr, tidyr in NAMESPACE as well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking vignette directory...
* WARNING: Evaluate more vignette chunks.
# of code chunks: 73
# of eval=FALSE: 43
# of nonexecutable code chunks by syntax: 29
# total unevaluated 72 (98%)
* WARNING: BiocInstaller code found in vignette(s)
Found in file(s):
seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd
(line 623)
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seqpac...
* WARNING: The following files call library or require on seqpac.
This is not necessary. man/add_reanno.Rd, man/as.PAC.Rd,
man/as.reanno.Rd, man/filtsep_bin.Rd, man/make_PAC.Rd,
man/PAC_filter.Rd, man/PAC_jitter.Rd, man/PAC_nbias.Rd,
man/PAC_norm.Rd, man/PAC_pca.Rd, man/PAC_saturation.Rd,
man/PAC_sizedist.Rd, man/PAC_stackbar.Rd, man/PAC_summary.Rd,
man/PAC.Rd, man/reanno.Rd
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
add_reanno.R (line 219, column 15)
add_reanno.R (line 224, column 17)
add_reanno.R (line 274, column 16)
add_reanno.R (line 291, column 15)
add_reanno.R (line 297, column 17)
add_reanno.R (line 418, column 49)
add_reanno.R (line 422, column 55)
filtsep_bin.R (line 72, column 15)
import_reanno.R (line 107, column 13)
import_reanno.R (line 171, column 51)
make_conv.R (line 132, column 12)
make_conv.R (line 167, column 14)
make_conv.R (line 204, column 12)
make_conv.R (line 268, column 14)
make_conv.R (line 270, column 40)
make_counts.R (line 346, column 35)
make_counts.R (line 419, column 35)
make_counts.R (line 483, column 40)
make_cutadapt.R (line 120, column 37)
make_pheno.R (line 206, column 16)
make_pheno.R (line 213, column 16)
make_reanno.R (line 182, column 16)
make_reanno.R (line 184, column 12)
make_reanno.R (line 236, column 14)
make_reanno.R (line 241, column 18)
make_reanno.R (line 268, column 15)
make_trim.R (line 202, column 42)
make_trim.R (line 257, column 7)
make_trim.R (line 366, column 18)
make_trim.R (line 575, column 53)
make_trim.R (line 605, column 14)
make_trim.R (line 618, 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 296, column 12)
map_reanno.R (line 303, column 15)
merge_lanes.R (line 86, column 30)
merge_lanes.R (line 93, column 14)
PAC_check.R (line 148, column 52)
PAC_check.R (line 157, column 54)
PAC_covplot.R (line 164, column 14)
PAC_covplot.R (line 183, column 14)
PAC_covplot.R (line 207, column 12)
PAC_covplot.R (line 213, column 36)
PAC_covplot.R (line 217, column 30)
PAC_covplot.R (line 225, column 54)
PAC_covplot.R (line 246, column 12)
PAC_deseq.R (line 133, column 13)
PAC_filter.R (line 252, column 17)
PAC_gtf.R (line 213, column 21)
PAC_gtf.R (line 231, column 13)
PAC_gtf.R (line 350, column 12)
PAC_gtf.R (line 375, column 12)
PAC_gtf.R (line 426, column 36)
PAC_gtf.R (line 457, column 12)
PAC_gtf.R (line 463, column 39)
PAC_gtf.R (line 505, column 14)
PAC_gtf.R (line 509, column 16)
PAC_gtf.R (line 521, column 14)
PAC_gtf.R (line 525, column 16)
PAC_jitter.R (line 168, column 22)
PAC_mapper.R (line 259, column 12)
PAC_mapper.R (line 319, column 12)
PAC_mapper.R (line 357, column 49)
PAC_mismap.R (line 148, column 12)
PAC_mismap.R (line 155, column 34)
PAC_mismap.R (line 163, column 11)
PAC_nbias.R (line 192, column 12)
PAC_norm.R (line 62, column 15)
PAC_pca.R (line 128, column 47)
PAC_pie.R (line 175, column 15)
PAC_pie.R (line 189, column 13)
PAC_pie.R (line 201, column 24)
PAC_pie.R (line 201, column 40)
PAC_saturation.R (line 83, column 41)
PAC_saturation.R (line 97, column 14)
PAC_saturation.R (line 161, 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 145, column 50)
PAC_trna.R (line 312, column 23)
PAC_trna.R (line 332, column 16)
progress_report.R (line 147, column 21)
simplify_reanno.R (line 188, column 23)
simplify_reanno.R (line 250, column 15)
simplify_reanno.R (line 268, column 12)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/make_cutadapt.R
(line 107, column 10)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/make_reanno.R (line
294, column 12)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/make_reanno.R (line
316, column 15)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/make_trim.R (line
230, column 10)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/map_reanno.R (line
254, column 13)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/map_reanno.R (line
259, column 12)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
90, column 10)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
94, column 10)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
130, column 16)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
136, column 16)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
152, column 22)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
161, column 24)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
180, column 17)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
200, column 11)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
214, column 17)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_check.R (line
223, column 20)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_gtf.R (line 293,
column 15)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_summary.R (line
108, column 12)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_filter.R (line
115, column 11)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_filter.R (line
227, column 12)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_filter.R (line
230, column 12)
/tmp/Rtmpqcy9iK/file1f989ec69383a/seqpac/R/PAC_gtf.R (line 337,
column 5)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 3
times)
T in R/PAC_mismap.R (line 180, column 22)
T in R/PAC_mismap.R (line 180, column 56)
T in R/PAC_mismap.R (line 217, column 30)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
check_reanno.R (line 36, column 41)
check_reanno.R (line 38, column 41)
check_reanno.R (line 40, column 41)
check_reanno.R (line 42, column 41)
make_PAC.R (line 72, column 19)
map_rangetype.R (line 285, column 24)
PAC_check.R (line 145, column 25)
PAC_check.R (line 146, column 24)
PAC_check.R (line 209, column 25)
PAC_check.R (line 210, column 24)
PAC_deseq.R (line 174, column 18)
PAC_filter.R (line 140, column 26)
PAC_gtf.R (line 210, column 17)
PAC_gtf.R (line 218, column 20)
PAC_mapper.R (line 176, column 16)
PAC_mapper.R (line 184, column 20)
PAC_trna.R (line 205, column 30)
PAC_trna.R (line 215, column 30)
PAC_trna.R (line 225, column 29)
progress_report.R (line 49, column 20)
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/as.PAC.Rd
Found @ in man/as.reanno.Rd
Found @ in man/PAC.Rd
Found @ in man/reanno.Rd
* 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 271, column 7)
suppressWarnings() in R/make_counts.R (line 198, column 7)
suppressWarnings() in R/make_cutadapt.R (line 95, column 5)
suppressWarnings() in R/make_trim.R (line 237, column 5)
suppressWarnings() in R/map_reanno.R (line 263, column 5)
suppressWarnings() in R/PAC_filter.R (line 259, column 7)
suppressWarnings() in R/PAC_gtf.R (line 318, column 13)
suppressWarnings() in R/PAC_gtf.R (line 475, column 17)
suppressWarnings() in R/PAC_mapper.R (line 205, column 3)
suppressWarnings() in R/PAC_mapper.R (line 209, column 3)
suppressMessages() in R/PAC_pca.R (line 109, column 12)
suppressMessages() in R/PAC_pca.R (line 113, column 12)
suppressWarnings() in R/PAC_trna.R (line 466, column 9)
* Checking function lengths................................................................................
* NOTE: Recommended function length <= 50 lines.
There are 35 functions > 50 lines.
The longest 5 functions are:
make_trim() (R/make_trim.R, line 166): 524 lines
make_counts() (R/make_counts.R, line 169): 379 lines
PAC_gtf() (R/PAC_gtf.R, line 196): 369 lines
PAC_trna() (R/PAC_trna.R, line 188): 366 lines
add_reanno() (R/add_reanno.R, line 189): 278 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/anno.Rd, man/colnames.Rd, man/counts.Rd, man/full.Rd,
man/length.Rd, man/names.Rd, man/ncol.Rd, man/norm.Rd,
man/nrow.Rd, man/overview.Rd, man/PAC.Rd, man/pheno.Rd,
man/rownames.Rd, man/show.Rd, man/summary.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
add_reanno.Rd, anno.Rd, counts.Rd, full.Rd, import_reanno.Rd,
make_conv.Rd, make_counts.Rd, make_cutadapt.Rd, make_pheno.Rd,
make_reanno.Rd, make_trim.Rd, map_rangetype.Rd, map_reanno.Rd,
merge_lanes.Rd, norm.Rd, overview.Rd, PAC_check.Rd, PAC_covplot.Rd,
PAC_deseq.Rd, PAC_filtsep.Rd, PAC_gtf.Rd, PAC_mapper.Rd,
PAC_mismap.Rd, PAC_pie.Rd, PAC_trna.Rd, pheno.Rd, progress_report.Rd,
simplify_reanno.Rd, summary.Rd, tRNA_class.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
45% of man pages use one of these cases.
Found in the following files:
add_reanno.Rd
check_reanno.Rd
filtsep_bin.Rd
import_reanno.Rd
make_conv.Rd
make_counts.Rd
make_cutadapt.Rd
make_pheno.Rd
make_reanno.Rd
make_trim.Rd
map_rangetype.Rd
map_reanno.Rd
merge_lanes.Rd
PAC_check.Rd
PAC_covplot.Rd
PAC_deseq.Rd
PAC_filtsep.Rd
PAC_gtf.Rd
PAC_mapper.Rd
PAC_mismap.Rd
PAC_pie.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
check_reanno.Rd
import_reanno.Rd
make_conv.Rd
make_counts.Rd
make_cutadapt.Rd
make_pheno.Rd
make_reanno.Rd
make_trim.Rd
map_rangetype.Rd
map_reanno.Rd
merge_lanes.Rd
PAC_check.Rd
PAC_covplot.Rd
PAC_deseq.Rd
PAC_filtsep.Rd
PAC_gtf.Rd
PAC_mapper.Rd
PAC_mismap.Rd
PAC_pie.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; 385 lines (2%) are > 80 characters
long.
First 6 lines:
R/add_reanno.R:115 #' Ensembl =c("lincRNA", "miRNA", "p...
R/add_reanno.R:116 #' "snRNA", "tRNA", "Uhg",...
R/add_reanno.R:123 #' reanno <- make_reanno(reanno_path=output_bio, PAC...
R/filtsep_bin.R:68 df <- as.data.frame(matrix(NA, nrow=length(seqs...
R/import_reanno.R:199 hits <- paste(uniqu...
R/make_conv.R:34 #' @param ref_path_A Character string with the path 1s...
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
First 3 lines:
R/PAC_covplot.R:301 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
* NOTE: Consider multiples of 4 spaces for line indents, 4775
lines(26%) are not.
First 6 lines:
R/add_reanno.R:190 bio_perfect=FALSE, genome_max...
R/add_reanno.R:191
R/add_reanno.R:192 if(isS4(reanno)){
R/add_reanno.R:195 }else{
R/add_reanno.R:197 }
R/add_reanno.R:198
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 4
WARNING count: 8
NOTE count: 15
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.