Christian Panse
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/specL |
| git_branch: RELEASE_3_16 |
| git_last_commit: 2415bca |
| git_last_commit_date: 2022-12-12 10:07:35 -0400 (Mon, 12 Dec 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:20 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 1932/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| specL 1.32.1 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: specL |
| Version: 1.32.1 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:specL.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings specL_1.32.1.tar.gz |
| StartedAt: 2023-04-11 00:13:21 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:14:19 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 58.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: specL.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:specL.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings specL_1.32.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/specL.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘specL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘specL’ version ‘1.32.1’
* 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 ‘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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
merge.specLSet plot.psm plot.psmSet summary.psmSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ...
‘report.Rmd’ using ‘UTF-8’... OK
‘specL.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/specL.Rcheck/00check.log’
for details.
specL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL specL ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 0.000660276412963867 minutes
start protein annotation ...
time taken: 0.000243330001831055 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: 0.235027313232422 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: 0.240489482879639 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: 0.225351572036743 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: 0.261530160903931 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: 0.0077509880065918 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: 0.011397123336792 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: 0.218666315078735 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: 0.237812757492065 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: 0.0116112232208252 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: 0.0114374160766602 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: 0.13173246383667 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: 0.143850326538086 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: 0.259015560150146 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: 0.136845827102661 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: 0.163357734680176 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: 0.287665843963623 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: 0.260616779327393 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: 0.245084524154663 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
RUNIT TEST PROTOCOL -- Tue Apr 11 00:13:59 2023
***********************************************
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
5.634 0.218 5.823
specL.Rcheck/specL-Ex.timings
| name | user | system | elapsed | |
| annotate.protein_id | 0.032 | 0.010 | 0.062 | |
| cdsw | 0.009 | 0.004 | 0.014 | |
| genSwathIonLib | 0.350 | 0.002 | 0.350 | |
| iRTpeptides | 0.004 | 0.000 | 0.004 | |
| peptideStd | 0.003 | 0.004 | 0.007 | |
| read.bibliospec | 0 | 0 | 0 | |
| specL-class | 0.001 | 0.000 | 0.001 | |
| specLSet-class | 0.001 | 0.000 | 0.001 | |