Vlad Petyuk
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/MSnID |
| Branch: RELEASE_3_12 |
| Last Commit: f0cef77 |
| Last Changed Date: 2020-10-27 10:59:05 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:22 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the MSnID package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1162/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSnID 1.24.0 (landing page) Vlad Petyuk
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSnID |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSnID_1.24.0.tar.gz |
| StartedAt: 2021-05-06 04:52:32 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:01:05 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 513.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSnID.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSnID_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSnID.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSnID' version '1.24.0'
* 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 'MSnID' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:83: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:104: file link 'proteins' in package 'MSnID' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:190: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnIDFilter-class.Rd:86: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/apply_filter.Rd:20: file link 'MSnIDFilter' in package 'MSnID' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/optimize_filter.Rd:48: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/optimize_filter.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/read_mzIDs.Rd:11: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSnID.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'BiocGenerics' 'BiocStyle' 'RUnit' 'ggplot2' 'msmsTests' 'xtable'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.read_mzIDs.mzR.engine.single.file: no visible binding for global
variable 'peptideRef'
Undefined global functions or variables:
peptideRef
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fetch_conversion_table 17.28 1.56 27.98
remap_accessions-method 11.25 0.54 12.30
remap_fasta_entry_names 10.57 0.60 12.56
optimize_filter 2.74 0.37 12.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fetch_conversion_table 18.05 1.10 19.92
remap_fasta_entry_names 6.56 0.34 7.17
remap_accessions-method 6.29 0.42 7.16
optimize_filter 2.59 0.22 15.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSnID.Rcheck/00check.log'
for details.
MSnID.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MSnID_1.24.0.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MSnID_1.24.0.zip && rm MSnID_1.24.0.tar.gz MSnID_1.24.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2619k 100 2619k 0 0 40.4M 0 --:--:-- --:--:-- --:--:-- 41.2M
install for i386
* installing *source* package 'MSnID' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MSnID'
finding HTML links ... done
MSnID-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:83: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:104: file link 'proteins' in package 'MSnID' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnID-class.Rd:190: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
MSnID-package html
MSnIDFilter-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/MSnIDFilter-class.Rd:86: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
accessions html
add_mod_symbol html
apply_filter html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/apply_filter.Rd:20: file link 'MSnIDFilter' in package 'MSnID' does not exist and so has been treated as a topic
assess_missed_cleavages html
assess_termini html
correct_peak_selection html
data html
evaluate_filter html
fetch_conversion_table html
id_quality html
infer_parsimonious_accessions html
map_mod_sites html
mass_measurement_error html
optimize_filter html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/optimize_filter.Rd:48: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/optimize_filter.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
peptides html
psms html
read_mzIDs html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpART3zf/R.INSTALL1a702d8a53fe/MSnID/man/read_mzIDs.Rd:11: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
recalibrate html
remap_accessions-method html
remap_fasta_entry_names html
report_mods html
** 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
install for x64
* installing *source* package 'MSnID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.24.0.zip
* DONE (MSnID)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked
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MSnID.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...
reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...
RUNIT TEST PROTOCOL -- Thu May 06 04:59:50 2021
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
36.75 2.01 50.28
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MSnID.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...
reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...
RUNIT TEST PROTOCOL -- Thu May 06 05:00:55 2021
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
43.32 1.17 64.67
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MSnID.Rcheck/examples_i386/MSnID-Ex.timings
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MSnID.Rcheck/examples_x64/MSnID-Ex.timings
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