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This page was generated on 2024-03-26 14:51:27 -0400 (Tue, 26 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
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Package 256/425HostnameOS / ArchINSTALLBUILDCHECK
msqc1 1.31.0  (landing page)
Christian Panse
Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/msqc1
git_branch: devel
git_last_commit: e5d8b0c
git_last_commit_date: 2023-10-24 09:13:41 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for msqc1 on nebbiolo1


To the developers/maintainers of the msqc1 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: msqc1
Version: 1.31.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:msqc1.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings msqc1_1.31.0.tar.gz
StartedAt: 2024-03-26 11:59:46 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 12:00:44 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 57.9 seconds
RetCode: 0
Status:   OK  
CheckDir: msqc1.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:msqc1.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings msqc1_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/msqc1.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
* checking for file ‘msqc1/DESCRIPTION’ ... OK
* this is package ‘msqc1’ version ‘1.31.0’
* checking package namespace information ... NOTE
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 ‘msqc1’ 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 code 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 ... NOTE
checkRd: (-1) msqc1-package.Rd:26: Lost braces; missing escapes or markup?
    26 |     \item \code{QTRAP} (ABSciex,  Concord,  Canada)  - {SRM mode}
       |                                                        ^
checkRd: (-1) msqc1-package.Rd:28: Lost braces; missing escapes or markup?
    28 |     \item \code{TSQvantage} (ThermoScientific,  Bremen,  Germany) - {SRM mode}
       |                                                                     ^
checkRd: (-1) msqc1-package.Rd:30: Lost braces; missing escapes or markup?
    30 |     \item \code{Qexactive} (ThermoScientific,  Bremen,  Germany) - {PRM mode}
       |                                                                    ^
checkRd: (-1) msqc1-package.Rd:32: Lost braces; missing escapes or markup?
    32 |     \item \code{QExactiveHF} (ThermoScientific,  Bremen,  Germany) - {DIA mode}
       |                                                                      ^
checkRd: (-1) msqc1-package.Rd:34: Lost braces; missing escapes or markup?
    34 |     \item \code{TRIPLETOF} 5600 (ABSciex,  Concord,  Canada) - {SWATH and MS1 mode}
       |                                                                ^
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/msqc1.Rcheck/00check.log’
for details.


Installation output

msqc1.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL msqc1
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘msqc1’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (msqc1)

Tests output

msqc1.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

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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.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(msqc1))
> 
> test_check("msqc1")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  0.589   0.073   0.652 

Example timings

msqc1.Rcheck/msqc1-Ex.timings

nameusersystemelapsed
msqc1-package0.0140.0040.018
msqc1_8rep0.0010.0000.001
msqc1_8rep_QEXACTIVEHF_assayDevel0.0000.0000.001
msqc1_8rep_tripleTOF5600_assayDevel0.0000.0010.001
msqc1_dil0.0000.0010.001
msqc1_userstudy0.0000.0010.000
peptides0.0000.0010.000