Back to Multiple platform build/check report for BioC 3.17
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-12-06 11:10:29 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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

BUILD results for specL on merida1


To the developers/maintainers of the specL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/specL.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.

raw results

Package 1910/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
specL 1.33.0  (landing page)
Christian Panse
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/specL
git_branch: master
git_last_commit: e129a09
git_last_commit_date: 2022-11-01 11:10:44 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: specL
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data specL
StartedAt: 2022-12-05 21:20:14 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 21:21:09 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 55.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data specL
###
##############################################################################
##############################################################################


* checking for file ‘specL/DESCRIPTION’ ... OK
* preparing ‘specL’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘report.Rmd’ using rmarkdown
Warning: All arguments to RSQLite Driver are ignored.
Warning: RSQLite::dbGetException() is deprecated, please switch to using standard error handling via tryCatch().
Warning: Closing open result set, pending rows
Warning in connection_release(conn@ptr) :
  There are 1 result in use. The connection will be released when they are closed
Warning: All arguments to RSQLite Driver are ignored.
Warning: Closing open result set, pending rows
Warning in connection_release(conn@ptr) :
  There are 1 result in use. The connection will be released when they are closed
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx  137
length of genSwathIonLibSpecL   137
time taken:  0.959965229034424 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 131
--- finished re-building ‘report.Rmd’

--- re-building ‘specL.Rnw’ using Sweave
start protein annotation ...
time taken:  0.000518552462259928 minutes
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx  137
length of genSwathIonLibSpecL   137
time taken:  0.749475002288818 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 137
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx  137
length of genSwathIonLibSpecL   137
time taken:  0.635331153869629 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 137
normalizing RT ...
no iRT peptides found for building the model.
=> no iRT regression applied, using orgiginal rt instead!
generating ion library ...
start generating specLSet object ...
length of findNN idx  129
length of genSwathIonLibSpecL   129
time taken:  0.72706413269043 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 129
writting specL object (including header) to file 'specL-Spectronaut.txt' ...
Error: processing vignette 'specL.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'specL.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.707   \item Time zone America/New_
                                    York
! LaTeX Error: Command \item invalid in math mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Command \item invalid in math mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.709   \item M
               atrix products: default
! Missing } inserted.
<inserted text> 
                }
l.709   \item M
               atrix products: default
! Extra }, or forgotten \endgroup.
\par ...m \@noitemerr {\@@par }\fi \else {\@@par }
                                                  \fi 
l.709   \item M
               atrix products: default
--- failed re-building 'specL.Rnw'

SUMMARY: processing the following file failed:
  'specL.Rnw'

Error: Vignette re-building failed.
Execution halted