Florian P Breitwieser
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/isobar |
| Branch: RELEASE_3_12 |
| Last Commit: 37cd3b5 |
| Last Changed Date: 2020-10-27 10:43:37 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:53 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the isobar package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 917/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| isobar 1.36.0 (landing page) Florian P Breitwieser
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: isobar |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings isobar_1.36.0.tar.gz |
| StartedAt: 2021-05-06 03:57:46 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:03:32 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 346.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: isobar.Rcheck |
| Warnings: 3 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings isobar_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/isobar.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 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' 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 'isobar' can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot")
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:175: 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/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:178: 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/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/isobar.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.as.matrix' '.as.vect' '.convertPeptideModif'
'.proteinGroupAsConciseDataFrame' '.read.idfile' '.sum.bool'
* checking S3 generic/method consistency ... WARNING
sequence:
function(nvec, ...)
sequence.coverage:
function(protein.group, protein.g, specificity, simplify, ...)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Found the following apparent S3 methods exported but not registered:
as.data.frame.IBSpectra as.data.frame.ProteinGroup plot.NoiseModel
sequence.coverage summary.ProteinGroup
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
.calcProbXGreaterThanY.orig: no visible global function definition for
'd'
.plot.pairs: possible error in
png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
Correlation plot", width = 1000, height = 1000, pointsize = 14):
unused argument (title = "Pairwise Correlation plot")
.read.peaklist: no visible binding for global variable 'type'
.round.distr: no visible global function definition for 'param'
.write.summarized.table: no visible binding for global variable 'name'
distrprint: no visible global function definition for 'param'
distrprint : <anonymous>: no visible global function definition for
'param'
shared.ratios.sign: no visible binding for global variable 'ratio'
shared.ratios.sign: no visible binding for global variable 'g'
spectra.count2: no visible binding for global variable 'peptide'
twodistr.plot: no visible global function definition for 'd'
ProteinGroup,data.frame-missing: no visible binding for global variable
'peptide'
coerce,IBSpectra-MSnSet: no visible global function definition for 'mz'
coerce,IBSpectra-MSnSet: no visible binding for global variable 'o'
coerce,MSnSet-IBSpectra: no visible global function definition for
'qual'
df,Tlsd: no visible global function definition for 'param'
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
visible binding for global variable 'i'
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
visible binding for global variable 'i'
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
global variable 'center.var'
location,Tlsd: no visible global function definition for 'param'
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable 'pch'
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable 'noise.model.col'
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable 'pch.p'
scale,Tlsd: no visible global function definition for 'param'
Undefined global functions or variables:
center.var d g i mz name noise.model.col o param pch pch.p peptide
qual ratio type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IBSpectra-class.Rd':
'[MSnbase]{MSnbase}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'peptide.count':
'sequence.coverage'
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 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
NoiseModel-class 11.61 0.1 11.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NoiseModel-class 13.56 0.06 13.62
* 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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/isobar.Rcheck/00check.log'
for details.
isobar.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/isobar_1.36.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL isobar_1.36.0.zip && rm isobar_1.36.0.tar.gz isobar_1.36.0.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 2190k 100 2190k 0 0 40.7M 0 --:--:-- --:--:-- --:--:-- 41.9M
install for i386
* installing *source* package 'isobar' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'coerce' with signature '"MSnSet","IBSpectra"': no definition for class "MSnSet"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "MSnSet"
Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot")
** help
*** installing help indices
converting help for package 'isobar'
finding HTML links ... done
IBSpectra-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:175: 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/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:178: 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/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic
NoiseModel-class html
ProteinGroup-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic
TlsParameter-class html
Tlsd-class html
calc.delta.score html
calc.startpos html
calculate-pvalues html
calculate.dNSAF html
calculate.emPAI html
correct.peptide.ratios html
distr-methods html
fit-distr html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpE3CGc4/R.INSTALL17c0b3d4cd8/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic
getPeptideModifContext html
getPhosphoRSProbabilities html
getPtmInfo html
groupMemberPeptides html
human.protein.names html
isobar-analysis html
isobar-data html
isobar-import html
isobar-log html
isobar-package html
isobar-plots html
isobar-preprocessing html
isobar-reports html
maplot.protein html
number.ranges html
observedKnownSites html
peptide.count html
proteinInfo-methods html
proteinNameAndDescription html
ratio-summ html
ratiosReshapeWide html
reporter.protein-methods html
sanitize html
shared.ratios html
shared.ratios.sign html
specificities html
spectra.count2 html
subsetIBSpectra html
utils html
writeHscoreData html
writeIBSpectra 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 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.36.0.zip
* DONE (isobar)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'isobar' successfully unpacked and MD5 sums checked
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isobar.Rcheck/examples_i386/isobar-Ex.timings
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isobar.Rcheck/examples_x64/isobar-Ex.timings
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