Devon Kohler
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: RELEASE_3_15 |
| git_last_commit: e7a3639 |
| git_last_commit_date: 2022-04-26 12:08:49 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:20 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 MSstatsPTM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.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 1263/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 1.6.0 (landing page) Devon Kohler
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstatsPTM |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_1.6.0.tar.gz |
| StartedAt: 2022-10-19 05:11:08 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 05:16:42 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 334.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsPTM’ 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 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
.format.data.process.plots: no visible binding for global variable
‘ABUNDANCE’
.plot.model.volcano: no visible binding for global variable
‘text.angle’
.progensis.add.sites: no visible binding for global variable
‘..col_order’
.qc.all.plot.lf: no visible binding for global variable ‘text.angle’
.qc.single.plot.lf: no visible binding for global variable ‘text.angle’
.rmConfounded: no visible binding for global variable ‘..col_res’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘PeptideSequence’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
‘Type’
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
‘R.Condition’
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
‘join_PeptideSequence’
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
‘PeptideSequence’
dataProcessPlotsPTM: no visible binding for global variable
‘PROTEINNAME’
dataProcessPlotsPTM: no visible binding for global variable
‘GLOBALPROTEIN’
dataSummarizationPTM: no visible binding for global variable ‘address’
locatePTM: no visible binding for global variable ‘..col_seq’
locatePTM: no visible binding for global variable ‘..col_fasta’
Undefined global functions or variables:
..col_fasta ..col_order ..col_res ..col_seq ABUNDANCE GLOBALPROTEIN
PROTEINNAME PeptideSequence R.Condition Type address
join_PeptideSequence text.angle
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
groupComparisonPlotsPTM 24.064 0.117 24.759
groupComparisonPTM 8.419 0.055 8.488
dataSummarizationPTM_TMT 8.258 0.117 8.398
dataProcessPlotsPTM 4.782 0.094 5.368
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘MSstatsPTM’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c model_adjustment.cpp -o model_adjustment.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsPTM)
MSstatsPTM.Rcheck/tests/tinytest.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstatsPTM")
+ }
test_dataSummarizationPTM.R... 0 tests
test_dataSummarizationPTM.R... 1 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 2 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 3 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 4 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 5 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 6 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 7 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 8 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 9 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 10 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 11 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 12 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 13 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 14 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 15 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 16 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 17 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 18 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 19 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 20 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 21 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 22 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 23 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 24 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 25 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 26 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 27 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 28 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 29 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 30 tests [0;32mOK[0m Starting PTM summarization...
test_dataSummarizationPTM.R... 31 tests [0;32mOK[0m [0;34m0.5s[0m
test_dataSummarizationPTM_TMT.R 0 tests
test_dataSummarizationPTM_TMT.R 1 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 2 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 3 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 4 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 5 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 6 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 7 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 8 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 9 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 10 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 11 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 12 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 13 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 14 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 15 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 16 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 17 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 18 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 19 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 20 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 21 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 22 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 23 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 24 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 25 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 26 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 27 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 28 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 29 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 30 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 31 tests [0;32mOK[0m [0;34m0.4s[0m
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 1 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 2 tests [0;32mOK[0m Starting PTM modeling...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m Starting PTM modeling...
INFO [2022-10-19 05:16:07] == Start to test and get inference in whole plot ...
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INFO [2022-10-19 05:16:14] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2022-10-19 05:16:14] == Start to test and get inference in whole plot ...
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INFO [2022-10-19 05:16:16] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 5 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 6 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 7 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 8 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling...
INFO [2022-10-19 05:16:16] Design: 2 mixtures.
INFO [2022-10-19 05:16:16] Design: 1 MS run per mixture.
INFO [2022-10-19 05:16:16] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2022-10-19 05:16:16] Model fitting for 90 proteins.
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INFO [2022-10-19 05:16:20] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2022-10-19 05:16:21] Design: 2 mixtures.
INFO [2022-10-19 05:16:21] Design: 1 MS run per mixture.
INFO [2022-10-19 05:16:21] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2022-10-19 05:16:21] Model fitting for 85 proteins.
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INFO [2022-10-19 05:16:31] Testing for 85 proteins:
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Starting adjustment...
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 11 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 12 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 13 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 14 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 15 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 16 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 17 tests [0;32mOK[0m [0;34m33.2s[0m
All ok, 79 results (34.1s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
44.934 0.843 45.832
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsPTMFormat | 0.076 | 0.004 | 0.084 | |
| ProgenesistoMSstatsPTMFormat | 0.213 | 0.003 | 0.234 | |
| SpectronauttoMSstatsPTMFormat | 0.154 | 0.001 | 0.170 | |
| annotSite | 0.000 | 0.000 | 0.001 | |
| dataProcessPlotsPTM | 4.782 | 0.094 | 5.368 | |
| dataSummarizationPTM | 4.141 | 0.072 | 4.305 | |
| dataSummarizationPTM_TMT | 8.258 | 0.117 | 8.398 | |
| groupComparisonPTM | 8.419 | 0.055 | 8.488 | |
| groupComparisonPlotsPTM | 24.064 | 0.117 | 24.759 | |
| locateMod | 0.001 | 0.000 | 0.000 | |
| locatePTM | 0.070 | 0.001 | 0.071 | |
| raw.input | 0.134 | 0.001 | 0.136 | |
| raw.input.tmt | 0.010 | 0.001 | 0.010 | |
| summary.data | 0.488 | 0.322 | 0.811 | |
| summary.data.tmt | 0.954 | 0.619 | 1.574 | |
| tidyFasta | 0.012 | 0.001 | 0.012 | |