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This page was generated on 2023-10-12 14:51:36 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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

Package 308/421HostnameOS / ArchINSTALLBUILDCHECK
qPLEXdata 1.18.0  (landing page)
Kamal Kishore Developer
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/qPLEXdata
git_branch: RELEASE_3_17
git_last_commit: 41c731c
git_last_commit_date: 2023-04-25 10:45:43 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  

CHECK results for qPLEXdata on nebbiolo1


To the developers/maintainers of the qPLEXdata package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: qPLEXdata
Version: 1.18.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:qPLEXdata.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings qPLEXdata_1.18.0.tar.gz
StartedAt: 2023-10-12 11:53:16 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:55:32 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 136.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: qPLEXdata.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:qPLEXdata.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings qPLEXdata_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/qPLEXdata.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘qPLEXdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qPLEXdata’ version ‘1.18.0’
* 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 ‘qPLEXdata’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘dplyr::combine’ by ‘MSnbase::combine’ when loading ‘qPLEXdata’
See ‘/home/biocbuild/bbs-3.17-data-experiment/meat/qPLEXdata.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
* 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 startup messages can be suppressed ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘qPLEXdata.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘qPLEXdata.Rnw’ using knitr

Quitting from lines 55-74 [exp1_specificity] (qPLEXdata.Rnw)
Error: processing vignette 'qPLEXdata.Rnw' failed with diagnostics:
statmod package required but is not installed
--- failed re-building ‘qPLEXdata.Rnw’

SUMMARY: processing the following file failed:
  ‘qPLEXdata.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/qPLEXdata.Rcheck/00check.log’
for details.


Installation output

qPLEXdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qPLEXdata
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘qPLEXdata’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘dplyr::combine’ by ‘MSnbase::combine’ when loading ‘qPLEXdata’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘dplyr::combine’ by ‘MSnbase::combine’ when loading ‘qPLEXdata’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘dplyr::combine’ by ‘MSnbase::combine’ when loading ‘qPLEXdata’
** testing if installed package keeps a record of temporary installation path
* DONE (qPLEXdata)

Tests output


Example timings

qPLEXdata.Rcheck/qPLEXdata-Ex.timings

nameusersystemelapsed
qPLEXdata0.0090.0000.010