| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:52 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BgeeCall package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BgeeCall.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 141/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BgeeCall 1.15.0 (landing page) Julien Wollbrett
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BgeeCall |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BgeeCall_1.15.0.tar.gz |
| StartedAt: 2023-02-06 18:33:17 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 18:41:57 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 519.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BgeeCall.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BgeeCall_1.15.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BgeeCall.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.15.0’
* 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 whether package ‘BgeeCall’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
extdata 8.7Mb
* checking package directory ... 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 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 ... NOTE
approachesMerging : <anonymous>: no visible global function definition
for ‘p.adjust’
generate_calls_workflow: no visible binding for global variable
‘myUserMetadata’
generate_qValue: no visible global function definition for ‘approxfun’
generate_qValue: no visible global function definition for ‘integrate’
generate_qValue : calculate_qValue: no visible global function
definition for ‘integrate’
generate_theoretical_pValue: no visible binding for global variable
‘abundance’
generate_theoretical_pValue: no visible binding for global variable
‘type’
generate_theoretical_pValue: no visible global function definition for
‘pnorm’
merging_libraries: no visible binding for global variable ‘read.delim’
should_ignore_tx_version: no visible global function definition for
‘complete.cases’
Undefined global functions or variables:
abundance approxfun complete.cases integrate myUserMetadata p.adjust
pnorm read.delim type
Consider adding
importFrom("stats", "approxfun", "complete.cases", "integrate",
"p.adjust", "pnorm")
importFrom("utils", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generate_presence_absence 5.363 0.152 13.155
setAnnotationFromFile 2.254 0.160 10.612
merge_transcriptome_and_intergenic 0.648 0.064 5.649
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘bgeecall-manual.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.
BgeeCall.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BgeeCall ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘BgeeCall’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (BgeeCall)
BgeeCall.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BgeeCall)
>
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeCall")
trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
31.724 1.062 73.027
BgeeCall.Rcheck/BgeeCall-Ex.timings
| name | user | system | elapsed | |
| create_kallisto_index | 0 | 0 | 0 | |
| download_fasta_intergenic | 0.000 | 0.002 | 0.002 | |
| download_kallisto | 0.505 | 0.097 | 4.368 | |
| generate_calls_workflow | 0 | 0 | 0 | |
| generate_presence_absence | 5.363 | 0.152 | 13.155 | |
| generate_slurm_calls | 0 | 0 | 0 | |
| generate_slurm_indexes | 0 | 0 | 0 | |
| getIntergenicPrefix | 0.160 | 0.000 | 1.113 | |
| getIntergenicRelease | 0.154 | 0.000 | 1.092 | |
| getRunIds | 0.001 | 0.000 | 0.001 | |
| getSimpleArborescence | 0 | 0 | 0 | |
| getWorkingPath | 0 | 0 | 0 | |
| list_bgee_ref_intergenic_species | 0.599 | 0.004 | 4.956 | |
| list_community_ref_intergenic_species | 0.162 | 0.000 | 1.711 | |
| list_intergenic_release | 0.183 | 0.004 | 1.016 | |
| merge_transcriptome_and_intergenic | 0.648 | 0.064 | 5.649 | |
| merging_libraries | 0 | 0 | 0 | |
| run_kallisto | 0.000 | 0.000 | 0.001 | |
| run_tximport | 2.084 | 0.012 | 2.893 | |
| setAnnotationFromFile | 2.254 | 0.160 | 10.612 | |
| setAnnotationFromObject | 0.209 | 0.000 | 3.752 | |
| setIntergenicRelease | 0.153 | 0.000 | 1.240 | |
| setOutputDir | 0 | 0 | 0 | |
| setRNASeqLibPath | 0.000 | 0.000 | 0.001 | |
| setRunIds | 0.000 | 0.000 | 0.001 | |
| setSimpleArborescence | 0 | 0 | 0 | |
| setTranscriptomeFromFile | 0.018 | 0.003 | 0.044 | |
| setTranscriptomeFromObject | 0.003 | 0.004 | 0.022 | |
| setWorkingPath | 0 | 0 | 0 | |