Christian Panse
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/specL |
| git_branch: RELEASE_3_18 |
| git_last_commit: 10a9664 |
| git_last_commit_date: 2023-10-24 10:40:13 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:21 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 2017/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| specL 1.36.0 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the specL package: - 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 Troubleshooting Build Report for more information. - 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. |
| Package: specL |
| Version: 1.36.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:specL.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings specL_1.36.0.tar.gz |
| StartedAt: 2024-03-28 05:26:13 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:27:08 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 54.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: specL.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:specL.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings specL_1.36.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/specL.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'specL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'specL' version '1.36.0'
* 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 whether package 'specL' 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 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 ... NOTE
.retentiontimePlotFile : <anonymous>: no visible global function
definition for 'head'
summary,specLSet : <anonymous>: no visible binding for global variable
'iRTpeptides'
Undefined global functions or variables:
head iRTpeptides
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* 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 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 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.18-bioc/meat/specL.Rcheck/00check.log'
for details.
specL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL specL ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'specL' ... ** 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 (specL)
specL.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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.
> BiocGenerics:::testPackage("specL")
Attaching package: 'specL'
The following objects are masked from 'package:protViz':
plot.psm, plot.psmSet, summary.psmSet
start protein annotation ...
time taken: 0.000229581197102865 minutes
start protein annotation ...
time taken: 9.91185506184896e-05 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: 0.212408781051636 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: 0.313811063766479 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: 0.226928949356079 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 137
length of genSwathIonLibSpecL 137
time taken: 0.256625175476074 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 ...
model with only one file.
generating ion library ...
start generating specLSet object ...
length of findNN idx 1
length of genSwathIonLibSpecL 1
time taken: 0.00214886665344238 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 1
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 ...
model with only one file.
generating ion library ...
start generating specLSet object ...
length of findNN idx 1
length of genSwathIonLibSpecL 1
time taken: 0.00238990783691406 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 1
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: 0.259298086166382 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 137
length of genSwathIonLibSpecL 137
time taken: 0.228822946548462 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 ...
model with only one file.
generating ion library ...
start generating specLSet object ...
length of findNN idx 1
length of genSwathIonLibSpecL 1
time taken: 0.00202393531799316 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 1
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 ...
model with only one file.
generating ion library ...
start generating specLSet object ...
length of findNN idx 1
length of genSwathIonLibSpecL 1
time taken: 0.00617694854736328 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 1
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 69
length of genSwathIonLibSpecL 69
time taken: 0.144794940948486 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 69
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 68
length of genSwathIonLibSpecL 68
time taken: 0.155048131942749 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 68
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: 0.220823049545288 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 69
length of genSwathIonLibSpecL 69
time taken: 0.119246959686279 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 69
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 68
length of genSwathIonLibSpecL 68
time taken: 0.106369018554688 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 68
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: 0.241197109222412 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
fetched 137 rows.
assigning 28 modifications ...
fetched 184 rows.
assigning 37 modifications ...
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: 0.270260810852051 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
fetched 137 rows.
assigning 28 modifications ...
fetched 184 rows.
assigning 37 modifications ...
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: 0.263043880462646 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
RUNIT TEST PROTOCOL -- Thu Mar 28 05:26:59 2024
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 0
1 Test Suite :
specL RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9
Number of errors: 0
Number of failures: 0
There were 13 warnings (use warnings() to see them)
>
>
> proc.time()
user system elapsed
5.82 0.25 6.04
specL.Rcheck/specL-Ex.timings
| name | user | system | elapsed | |
| annotate.protein_id | 0.01 | 0.00 | 0.01 | |
| cdsw | 0.01 | 0.00 | 0.01 | |
| genSwathIonLib | 0.31 | 0.00 | 0.31 | |
| iRTpeptides | 0.00 | 0.02 | 0.02 | |
| peptideStd | 0.02 | 0.00 | 0.01 | |
| read.bibliospec | 0 | 0 | 0 | |
| specL-class | 0 | 0 | 0 | |
| specLSet-class | 0 | 0 | 0 | |