===============================
BiocCheckGitClone('Ribostan')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: Ribostan
PackageVersion: 0.99.9
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2448/570185fe888ad21f77a14fc7a018663021bbc456/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: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'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/2448/570185fe888ad21f77a14fc7a018663021bbc456/Ribostan.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* 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 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file Ribostan/DESCRIPTION ... OK
* this is package Ribostan version 0.99.9
* 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 code 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 ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] 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 ... [35s/35s] 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [129s/129s] ERROR
Running examples in Ribostan-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_codon_occs
> ### Title: Estimate per codon occupancies
> ### Aliases: get_codon_occs
> ### Keywords: Ribostan
>
> ### ** Examples
>
> data(chr22_anno)
> data(rpfs)
> data(offsets_df)
> fafile <- here::here('chr22.fa')
> Rsamtools::indexFa(fafile)
[1] "/home/pkgbuild/packagebuilder/chr22.fa.fai"
> library(BSgenome.Hsapiens.UCSC.hg38)
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Attaching package: BiocGenerics
The following objects are masked from package:stats:
IQR, mad, sd, var, xtabs
The following objects are masked from package:base:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: S4Vectors
The following object is masked from package:utils:
findMatches
The following objects are masked from package:base:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: Biostrings
The following object is masked from package:base:
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: rtracklayer
The following object is masked from package:BiocIO:
FileForFormat
> if(!file.exists(fafile)){
+ seq <- Biostrings::DNAStringSet(BSgenome.Hsapiens.UCSC.hg38[['chr22']])
+ names(seq) <- 'chr22'
+ Biostrings::writeXStringSet(
+ seq, fafile)}
> psites <- get_psite_gr(rpfs, offsets_df, chr22_anno)
> rust_codon_occ_df <- get_codon_occs(psites, offsets_df, chr22_anno,
+ n_genes = 200, method = "RUST"
+ )
Warning in file(file, "r") :
cannot open file 'chr22.fa.fai': No such file or directory
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': cannot open the connection
Calls: get_codon_occs ... scanFaIndex -> scan -> file -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [281s/282s]
[282s/283s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
finished filtering ourfs
uORFs found
getting codon positions...
......running multitaper tests, this will be slow for a full dataset...
Adding missing grouping variables: `readlen`
Adding missing grouping variables: `readlen`
optimizing...
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 43 ]
Failed tests
Error ('test-quant.R:15:3'): test optimisation of quantification works
Error in `eval(code, test_env)`: object 'ms_df' not found
Backtrace:
1. ... %>% filter(ribo > 0) at test-quant.R:15:3
2. dplyr::filter(., ribo > 0)
3. dplyr::filter(., is.finite(log2(expr)))
4. dplyr::left_join(., gritpms)
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 43 ]
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, 1 WARNING, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/2448/570185fe888ad21f77a14fc7a018663021bbc456/Ribostan.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('Ribostan_0.99.9.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: Ribostan
PackageVersion: 0.99.9
sourceDir: /tmp/Rtmp3WhR1x/file3f8dd362b8d247/Ribostan
installDir: /tmp/Rtmp3WhR1x/file3f8dd3323a6d48
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2448/570185fe888ad21f77a14fc7a018663021bbc456/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...
* Checking for recommended DESCRIPTION fields...
* 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 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.
* 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; 58 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 977 lines
(33%) 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 | 9 NOTES
See the Ribostan.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.