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R CMD BUILD
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* checking for file ‘txdbmaker/DESCRIPTION’ ... OK
* preparing ‘txdbmaker’:
* 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
* building ‘txdbmaker_0.99.3.tar.gz’
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BiocCheckGitClone('txdbmaker')
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─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: txdbmaker
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3226/7130ac1b355911592e878f469a5cbf069b4be788/txdbmaker
─ 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')
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3226/7130ac1b355911592e878f469a5cbf069b4be788/txdbmaker.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 ‘txdbmaker/DESCRIPTION’ ... OK
* this is package ‘txdbmaker’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'AnnotationDbi', 'GenomicRanges', 'GenomicFeatures'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘txdbmaker’ 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] 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 ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::dbEasyQuery’ ‘BiocGenerics:::testPackage’
‘GenomeInfoDb:::check_tax_id’
‘GenomeInfoDb:::lookup_organism_by_tax_id’
‘GenomeInfoDb:::lookup_tax_id_by_organism’
‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
‘S4Vectors:::anyMissingOrOutside’
‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
‘rtracklayer:::resourceDescription’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [40s/40s] OK
* 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 Rd file 'txdbmaker-package.Rd':
‘https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [95s/232s] ERROR
Running examples in ‘txdbmaker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ### database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
>
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database:
> library(biomaRt)
> listMarts(host="https://www.ensembl.org")
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 111
2 ENSEMBL_MART_MOUSE Mouse strains 111
3 ENSEMBL_MART_SNP Ensembl Variation 111
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 111
> mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org")
> datasets <- listDatasets(mart)
> head(datasets)
[1] dataset description version
<0 rows> (or 0-length row.names)
> subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
[1] dataset description version
<0 rows> (or 0-length row.names)
>
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
Error in checkDataset(dataset = dataset, mart = mart) :
The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
Calls: makeTxDbFromBiomart ... .useMart2 -> useEnsembl -> useDataset -> checkDataset
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’ [53s/54s]
[54s/54s] ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 20 lines of output:
The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
Test files with failing tests
test_makeTxDbFromBiomart.R
test_makeTxDbFromBiomart
Error in BiocGenerics:::testPackage("txdbmaker") :
unit tests failed for package txdbmaker
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
exon. This information was ignored.
2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
3: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
the transcript names ("tx_name" column in the TxDb object) imported
from the "Name" attribute are not unique
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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3226/7130ac1b355911592e878f469a5cbf069b4be788/txdbmaker.Rcheck/00check.log’
for details.
===============================
BiocCheck('txdbmaker_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: txdbmaker
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/RtmpBIhfqL/file2782215438f58c/txdbmaker
─ installDir: /tmp/RtmpBIhfqL/file27822111127349
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3226/7130ac1b355911592e878f469a5cbf069b4be788/txdbmaker.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...
* 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...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Microarray, GO
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (65%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of txdbmaker...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 27 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 22% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 4 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1466 lines
(17%) 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 ──
0 ERRORS | 0 WARNINGS | 11 NOTES
See the txdbmaker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.