===============================
R CMD BUILD
===============================
* checking for file ‘Ribostan/DESCRIPTION’ ... OK
* preparing ‘Ribostan’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘Ribostan_0.99.7.tar.gz’
===============================
BiocCheckGitClone('Ribostan')
===============================
─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: Ribostan
─ PackageVersion: 0.99.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2448/1c925c79edd94daf9d35f23f83489c6323b7af46/Ribostan
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: No CITATION file found. Bioconductor packages are not
required to have a CITATION file but it is useful both for users
and for tracking Bioconductor project-wide metrics. If you later
post a preprint or publish a paper about your Bioconductor
package, please add the details with a 'doi' argument in the
CITATION file's 'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2448/1c925c79edd94daf9d35f23f83489c6323b7af46/Ribostan.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ribostan/DESCRIPTION’ ... OK
* this is package ‘Ribostan’ version ‘0.99.7’
* 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 ‘Ribostan’ can be installed ... 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘methods’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [36s/36s] NOTE
convert_gtf: no visible binding for global variable ‘Parent’
convert_gtf: no visible binding for global variable ‘type’
convert_gtf: no visible global function definition for ‘as’
export_codon_dts: no visible binding for global variable ‘nreadlen’
export_codon_dts: no visible binding for global variable ‘position’
export_codon_dts: no visible binding for global variable ‘site’
ftest_orfs: no visible binding for global variable ‘.’
ftestvect: no visible binding for global variable ‘.’
ftestvect: no visible global function definition for ‘as.ts’
ftestvect: no visible global function definition for ‘pf’
ftestvect: no visible binding for global variable ‘vals’
gene_level_elong: no visible binding for global variable ‘uORF’
gene_level_elong: no visible binding for global variable ‘.’
gene_level_elong: no visible binding for global variable ‘orf_id’
gene_level_elong: no visible global function definition for
‘weighted.mean’
gene_level_elong: no visible binding for global variable ‘mean_occ’
gene_level_elong: no visible binding for global variable ‘ritpm’
gene_level_expr: no visible binding for global variable ‘uORF’
get_cds_codons: no visible binding for global variable ‘.’
get_cds_reads: no visible global function definition for ‘head’
get_cds_reads: no visible binding for global variable ‘readlen’
get_cds_reads: no visible binding for global variable ‘readlens’
get_cdsgrl: no visible binding for global variable ‘.’
get_cdsgrl: no visible binding for global variable ‘type’
get_codon_occs: no visible binding for global variable ‘.’
get_codon_occs: no visible global function definition for ‘tail’
get_codon_occs: no visible binding for global variable ‘orf’
get_codon_occs: no visible global function definition for ‘glm.nb’
get_codon_occs: no visible binding for global variable ‘trmean’
get_codon_occs: no visible binding for global variable ‘rust’
get_codon_occs: no visible global function definition for ‘glm’
get_codon_occs: no visible global function definition for ‘setNames’
get_codposdf: no visible binding for global variable ‘.’
get_codposdf : <anonymous>: no visible binding for global variable ‘.’
get_codposdf: no visible binding for global variable ‘head’
get_cov_rust_scores : <anonymous>: no visible binding for global
variable ‘.’
get_exprfile: no visible global function definition for ‘setNames’
get_incl_max_offsets: no visible binding for global variable
‘startoffset’
get_incl_max_offsets: no visible binding for global variable ‘readlen’
get_incl_max_offsets: no visible binding for global variable ‘.’
get_metacodon_profs: no visible global function definition for
‘installed.packages’
get_offsets: no visible global function definition for ‘is’
get_orf_elong: no visible binding for global variable ‘.’
get_orf_elong : <anonymous>: no visible binding for global variable
‘orf_id’
get_orf_elong : <anonymous> : <anonymous>: no visible binding for
global variable ‘position’
get_orf_elong : <anonymous> : <anonymous>: no visible binding for
global variable ‘orf_id’
get_orf_elong : <anonymous> : <anonymous>: no visible global function
definition for ‘weighted.mean’
get_psite_gr: no visible binding for global variable ‘.’
get_psite_gr: no visible binding for global variable ‘p_offset’
get_psitecov: no visible binding for global variable ‘.’
get_readlens: no visible binding for global variable ‘.’
get_ribofasta_anno: no visible global function definition for
‘setNames’
get_ritpms: no visible binding for global variable ‘orf’
get_sitedf: no visible binding for global variable ‘.’
get_sitedf: no visible global function definition for ‘stack’
get_trspace_cds: no visible binding for global variable ‘.’
get_trspace_cds: no visible binding for global variable ‘transcript_id’
hasMstart: no visible binding for global variable ‘.’
is_out_of_bounds: no visible global function definition for ‘is’
load_annotation: no visible global function definition for ‘is’
load_annotation: no visible binding for global variable ‘transcript_id’
load_annotation: no visible binding for global variable ‘type’
load_annotation: no visible global function definition for ‘setNames’
make_ext_fasta: no visible binding for global variable ‘transcript_id’
make_ext_fasta: no visible binding for global variable ‘gene_id’
make_ext_fasta: no visible binding for global variable ‘gene_name’
mergeseqlevels: no visible global function definition for ‘as’
most_freq: no visible global function definition for ‘tail’
optimize_ritpms: no visible global function definition for ‘setNames’
optimize_ritpms: no visible binding for global variable ‘.’
periodicity_filter_uORFs: no visible binding for global variable ‘.’
plot_kl_dv: no visible binding for global variable ‘.’
plot_kl_dv: no visible binding for global variable ‘position’
plot_kl_dv: no visible binding for global variable ‘KL’
plot_kl_dv: no visible binding for global variable ‘p_offset’
read_ribobam: no visible global function definition for ‘as’
sample_cols_spmat: no visible global function definition for ‘tail’
sample_cols_spmat: no visible global function definition for ‘runif’
sample_cov_gr: no visible binding for global variable ‘.’
spl_mapFromTranscripts: no visible binding for global variable ‘.’
subset_annotation: no visible binding for global variable
‘transcript_id’
width1grs: no visible global function definition for ‘as’
Undefined global functions or variables:
. KL Parent as as.ts gene_id gene_name glm glm.nb head
installed.packages is mean_occ nreadlen orf orf_id p_offset pf
position readlen readlens ritpm runif rust setNames site stack
startoffset tail transcript_id trmean type uORF vals weighted.mean
Consider adding
importFrom("methods", "as", "is")
importFrom("stats", "as.ts", "glm", "pf", "runif", "setNames",
"weighted.mean")
importFrom("utils", "head", "installed.packages", "stack", "tail")
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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'addphase.Rd'
‘gr’
Documented arguments not in \usage in Rd file 'addphase.Rd':
‘rpfs’
Undocumented arguments in Rd file 'convert_gtf.Rd'
‘anno’
Documented arguments not in \usage in Rd file 'convert_gtf.Rd':
‘an’
Undocumented arguments in Rd file 'fmcols.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_cds_codons.Rd':
‘offsets_df’
Undocumented arguments in Rd file 'get_cds_reads.Rd'
‘anno’
Documented arguments not in \usage in Rd file 'get_cds_reads.Rd':
‘strip_seqnames’
Undocumented arguments in Rd file 'get_cdsgrl.Rd'
‘ignore_orf_validity’
Undocumented arguments in Rd file 'get_kl_df.Rd'
‘anno’
Undocumented arguments in Rd file 'get_metacodon_profs.Rd'
‘covgrs’ ‘n_wind_l_ext’
Documented arguments not in \usage in Rd file 'get_metacodon_profs.Rd':
‘rpf_covs’
Documented arguments not in \usage in Rd file 'get_psitecov.Rd':
‘orfnames’
Undocumented arguments in Rd file 'get_read_spmat.Rd'
‘anno’
Undocumented arguments in Rd file 'get_readgr.Rd'
‘offsets_df’
Undocumented arguments in Rd file 'get_trspace_cds.Rd'
‘cdsgrl’
Documented arguments not in \usage in Rd file 'get_trspace_cds.Rd':
‘trspacegr’
Undocumented arguments in Rd file 'hasMstart.Rd'
‘cdsgrl’ ‘fafileob’
Documented arguments not in \usage in Rd file 'hasMstart.Rd':
‘trspacegr’ ‘exonsgrl’
Undocumented arguments in Rd file 'is_out_of_bounds.Rd'
‘gr’ ‘si’
Documented arguments not in \usage in Rd file 'is_out_of_bounds.Rd':
‘grl’
Undocumented arguments in Rd file 'load_annotation.Rd'
‘fafile’ ‘ignore_orf_validity’
Documented arguments not in \usage in Rd file 'load_annotation.Rd':
‘fafileob’
Undocumented arguments in Rd file 'read_ribobam.Rd'
‘which’
Undocumented arguments in Rd file 'resize_grl.Rd'
‘fix’ ‘check’
Undocumented arguments in Rd file 'resize_grl_endfix.Rd'
‘width’
Undocumented arguments in Rd file 'select_offsets.Rd'
‘kl_df’
Documented arguments not in \usage in Rd file 'select_offsets.Rd':
‘metacodondf’
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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘Ribostan-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: export_codon_dts
> ### Title: Create a dataframe with a_site, p_site and e site occupancies
> ### Aliases: export_codon_dts
> ### Keywords: Ribostan
>
> ### ** Examples
>
> data(chr22_anno)
Warning in data(chr22_anno) : data set ‘chr22_anno’ not found
> data(rpfs)
Warning in data(rpfs) : data set ‘rpfs’ not found
> data(offsets_df)
Warning in data(offsets_df) : data set ‘offsets_df’ not found
> data(metacodondf)
Warning in data(metacodondf) : data set ‘metacodondf’ not found
> # note this doesn't work that well on a small subset
> kl_df <- get_kl_df(metacodondf, chr22_anno)
Error: object 'metacodondf' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [82s/83s]
[82s/83s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
3. │ ├─BiocGenerics::union(seqlevels(gr1), seqlevels(gr2))
4. │ └─GenomeInfoDb::seqlevels(gr1)
5. ├─base::.handleSimpleError(...)
6. │ └─base (local) h(simpleError(msg, call))
7. └─base::.handleSimpleError(...)
8. └─base (local) h(simpleError(msg, call))
── Error ('test-quant.R:8:3'): test optimisation of quantification works ───────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'union': error in evaluating the argument 'x' in selecting a method for function 'seqlevels': object 'rpfs' not found
Backtrace:
▆
1. ├─Ribostan::get_psite_gr(rpfs, offsets_df, chr22_anno) at test-quant.R:8:3
2. │ └─Ribostan:::mergeseqlevels(rpfs, orfs)
3. │ ├─BiocGenerics::union(seqlevels(gr1), seqlevels(gr2))
4. │ └─GenomeInfoDb::seqlevels(gr1)
5. ├─base::.handleSimpleError(...)
6. │ └─base (local) h(simpleError(msg, call))
7. └─base::.handleSimpleError(...)
8. └─base (local) h(simpleError(msg, call))
[ FAIL 6 | WARN 22 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2448/1c925c79edd94daf9d35f23f83489c6323b7af46/Ribostan.Rcheck/00check.log’
for details.
===============================
BiocCheck('Ribostan_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: Ribostan
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/Rtmp8XiXz0/file370886bcf4466/Ribostan
─ installDir: /tmp/Rtmp8XiXz0/file37088614c81377
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2448/1c925c79edd94daf9d35f23f83489c6323b7af46/Ribostan.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* WARNING: Package files exceed the 5MB size limit.
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (46%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Ribostan...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid system() ; use system2()
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 9 functions greater than 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 4% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 59 lines (2%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 21 lines (1%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 965 lines
(32%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
─ BiocCheck results ──
2 ERRORS | 1 WARNINGS | 15 NOTES
See the Ribostan.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.