| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:34 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the FoldGO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FoldGO.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 729/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FoldGO 1.19.0 (landing page) Daniil Wiebe
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: FoldGO |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FoldGO.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FoldGO_1.19.0.tar.gz |
| StartedAt: 2023-05-30 07:36:25 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 07:39:24 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 179.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: FoldGO.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FoldGO.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FoldGO_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FoldGO.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FoldGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FoldGO’ version ‘1.19.0’
* 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 ‘FoldGO’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... WARNING
checkRd: (5) fagroupstopgo_class.Rd:16: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:17: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:18-19: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:20-21: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:22: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:23: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:26-27: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:28-29: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:30-31: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:32-33: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:42: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:21: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:22: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:23: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:24-25: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:26-27: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:19: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:20: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:28: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:29: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:37-38: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:24-25: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:35-36: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:37-38: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:39: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:41: \item in \describe must have non-empty label
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot-FoldSpecTest-ANY-method 7.096 0.064 7.160
fagroupstopgo_class 6.068 0.268 6.337
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 119-121 [human_annot] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
package org.Hs.eg.db is required
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/home/biocbuild/bbs-3.18-bioc/meat/FoldGO.Rcheck/00check.log’
for details.
FoldGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL FoldGO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘FoldGO’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘getAnnotation’ with signature ‘"MgsaSets"’: no definition for class “MgsaSets” ** 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 (FoldGO)
FoldGO.Rcheck/FoldGO-Ex.timings
| name | user | system | elapsed | |
| examdata_bg | 0.002 | 0.000 | 0.003 | |
| examdata_degs | 0.001 | 0.000 | 0.002 | |
| examdata_objs | 0.002 | 0.000 | 0.002 | |
| fagroupstopgo_class | 6.068 | 0.268 | 6.337 | |
| foldspectest_class | 3.971 | 0.076 | 4.047 | |
| gafreader_class | 2.305 | 0.336 | 2.641 | |
| genegroups_class | 0.019 | 0.016 | 0.035 | |
| getAnnotation | 0 | 0 | 0 | |
| getWholeIntName | 3.702 | 0.076 | 3.777 | |
| plot-FoldSpecTest-ANY-method | 7.096 | 0.064 | 7.160 | |