Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	869
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CHECK results for mzID on teran2

To the developers/maintainers of the mzID 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: mzID

Version: 1.45.0

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:mzID.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings mzID_1.45.0.tar.gz

StartedAt: 2025-03-22 07:06:34 -0400 (Sat, 22 Mar 2025)

EndedAt: 2025-03-22 07:11:00 -0400 (Sat, 22 Mar 2025)

EllapsedTime: 265.8 seconds

RetCode: 1

Status: ERROR

CheckDir: mzID.Rcheck

Warnings: NA

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:mzID.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings mzID_1.45.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/mzID.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mzID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzID’ version ‘1.45.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzID’ 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 ... NOTE
mzID: no visible binding for global variable ‘i’
Undefined global functions or variables:
  i
* checking Rd files ... NOTE
checkRd: (-1) mzID-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mzID-package.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mzID-package.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mzID-package.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mzID-package.Rd:24-25: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
S3 methods shown with full name in Rd file 'mzIDCollection-class.Rd':
  ‘as.list.mzIDCollection’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘mzID-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mzID
> ### Title: Parse an mzIdentML file
> ### Aliases: mzID
> 
> ### ** Examples
> 
> 
> # Parsing of the example files provided by HUPO:
> exampleFiles <- list.files(system.file('extdata', package = 'mzID'), 
+                            pattern = '*.mzid', full.names = TRUE)
> mzID(exampleFiles[1])
reading 55merge_omssa.mzid... DONE!
An mzID object

Software used:   OMSSA (version: NA)

Rawfile:         D:/TestSpace/NeoTestMarch2011/55merge.mgf

Database:        D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta

Number of scans: 39
Number of PSM's: 99
> 
> mzID(exampleFiles[2])
reading 55merge_tandem.mzid... DONE!
An mzID object

Software used:   X\!Tandem (version: x! tandem CYCLONE (2010.06.01.5))

Rawfile:         D:/TestSpace/NeoTestMarch2011/55merge.mgf

Database:        D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta.pro

Number of scans: 169
Number of PSM's: 170
> 
> mzID(exampleFiles[3])
reading MPC_example_Multiple_search_engines.mzid... DONE!
An mzID object

Software used:   Sequest (version: PVM Slave v.27 (rev. 12))
                 Mascot (version 2.2.0)
                 ProteinScape (version NA)

Rawfile:         proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X

Database:        file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta

Number of scans: 18
Number of PSM's: 22
> 
> mzID(exampleFiles[4])
reading Mascot_MSMS_example.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
 DONE!
An mzID object

Software used:   Mascot (version: 2.2.03)
                 Mascot Parser (version 2.3.0.0)

Rawfile:         file:///dyckall.asc

Database:        file:///C:/inetpub/mascot/sequence/SwissProt/current/SwissProt_51.6.fasta

Number of scans: 4
Number of PSM's: 40
> 
> mzID(exampleFiles[5])
reading Mascot_MSMS_example1.0.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
 DONE!
An mzID object

Software used:   Mascot (version: 2.2.03)
                 Mascot Parser (version 2.3.0.0)

Rawfile:         file:///dyckall.asc

Database:        file:///C:/inetpub/mascot/sequence/SwissProt/current/SwissProt_51.6.fasta

Number of scans: 4
Number of PSM's: 40
> 
> mzID(exampleFiles[6])
reading Mascot_NA_example.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
 DONE!
An mzID object

Software used:   Mascot (version: 2.2.03)
                 Mascot Parser (version 2.3.0.0)

Rawfile:         file:///est_coding_test.mgf

Database:        file:///C:/inetpub/mascot/sequence/EST_mini/current/EST_mini_20080623.fasta

Number of scans: 4
Number of PSM's: 4
> 
> mzID(exampleFiles[7])
reading Mascot_top_down_example.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
 DONE!
An mzID object

Software used:   Mascot (version: 2.2.03)
                 Mascot Parser (version 2.3.0.0)

Rawfile:         file:///MYOGLOBIN_ECD.mgf

Database:        file:///C:/inetpub/mascot/sequence/SwissProt/current/SwissProt_51.6.fasta

Number of scans: 1
Number of PSM's: 5
> 
> mzID(exampleFiles[8])
reading Sequest_example_ver1.1.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in mzIDpsm(doc, ns, addFinalizer = addFinalizer) :
  NAs introduced by coercion
 DONE!
An mzID object

Software used:   Sequest (version: PVM Master v.27 (rev. 12), (c) 1998-2007)

Rawfiles:        file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.187.257.1.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.2.69.1.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.282.282.1.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.505.808.1.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.687.687.2.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.687.687.3.dta
                 file://www.medizinisches-proteom-center.de/martinlap/C/Eisi/MPC/ProCon/SEQUEST/example_folder/PMXPWE080620_38.693.693.2.dta

Database:        file://www.medizinisches-proteom-center.de/sequestmaster/work/Datenbank/StdCry_nr.fasta

Number of scans: 7
Number of PSM's: 88
> 
> mzID(exampleFiles[9])
reading mascot_pmf_example.mzid...Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in mzIDpsm(doc, ns, addFinalizer = addFinalizer) :
  NAs introduced by coercion
 DONE!
An mzID object

Software used:   Mascot (version: 2.3.02)
                 Mascot Parser (version 2.3.3.0)

Rawfile:         file:///

Database:        file:////usr/local/mascot/sequence/SwissProt/current/SwissProt_57.15.fasta

Number of scans: 1
Number of PSM's: 629
> 
> # Parsing into an mzIDCollection
> collection <- mzID(exampleFiles[1:3])
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
Error in makePSOCKcluster(names = spec, ...) : 
  Cluster setup failed. 3 of 3 workers failed to connect.
Calls: mzID -> makeCluster -> makePSOCKcluster
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘HOWTO_mzID.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/mzID.Rcheck/00check.log’
for details.

Installation output

mzID.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL mzID
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘mzID’ ...
** this is package ‘mzID’ version ‘1.45.0’
** 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 (mzID)

Tests output

mzID.Rcheck/tests/test-all.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

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)
> 
> test_check('mzID')
Loading required package: mzID
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  0.749   0.138   0.878

Example timings

mzID.Rcheck/mzID-Ex.timings

name	user	system	elapsed
flatten	0.254	0.030	0.291