Devon Kohler
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: RELEASE_3_16 |
| git_last_commit: 12af477 |
| git_last_commit_date: 2023-02-28 10:00:15 -0400 (Tue, 28 Feb 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:16 -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 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 1287/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.0.3 (landing page) Devon Kohler
| 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: MSstatsPTM |
| Version: 2.0.3 |
| 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_2.0.3.tar.gz |
| StartedAt: 2023-04-10 21:25:17 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:28:17 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 180.4 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_2.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘2.0.3’
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’
‘MSstatsConvert:::.filterFewMeasurements’
‘MSstatsConvert:::.filterManyColumns’
‘MSstatsConvert:::.getChannelColumns’
‘MSstatsConvert:::.standardizeColnames’
See the note in ?`:::` about the use of this operator.
* 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’
.pivotPS: no visible binding for global variable ‘..keep_cols’
.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’
.removeCutoffSites: no visible binding for global variable
‘..mod_pep_col’
.rmConfounded: no visible binding for global variable ‘..col_res’
MSstatsPTMSiteLocator: no visible binding for global variable
‘..mod_pep_col’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘TMT.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘ptm.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘mod.num’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘which.proteinid.ptm’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘PeptideSequence’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘annotation.prot’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘proteinGroups_prot’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘MSstatsPTMTMT.abun’
PStoMSstatsPTMFormat: no visible binding for global variable
‘Intensity’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
‘Type’
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 ..keep_cols ..mod_pep_col
ABUNDANCE GLOBALPROTEIN Intensity MSstatsPTMTMT.abun PROTEINNAME
PeptideSequence TMT.keyword Type address annotation.prot mod.num
proteinGroups_prot ptm.keyword text.angle which.proteinid.ptm
* 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 11.213 0.101 11.41
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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;34m0.2s[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;34m0.2s[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 [2023-04-10 21:27:56] == Start to test and get inference in whole plot ...
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INFO [2023-04-10 21:28:00] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2023-04-10 21:28:00] == Start to test and get inference in whole plot ...
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INFO [2023-04-10 21:28:00] == 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 [2023-04-10 21:28:00] Design: 2 mixtures.
INFO [2023-04-10 21:28:00] Design: 1 MS run per mixture.
INFO [2023-04-10 21:28:00] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-04-10 21:28:00] Model fitting for 90 proteins.
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INFO [2023-04-10 21:28:02] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2023-04-10 21:28:03] Design: 2 mixtures.
INFO [2023-04-10 21:28:03] Design: 1 MS run per mixture.
INFO [2023-04-10 21:28:03] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-04-10 21:28:03] Model fitting for 85 proteins.
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INFO [2023-04-10 21:28:07] 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;34m15.2s[0m
All ok, 79 results (15.6s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
20.851 0.565 21.486
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| MSstatsPTMSiteLocator | 0 | 0 | 0 | |
| MaxQtoMSstatsPTMFormat | 0.058 | 0.006 | 0.064 | |
| PDtoMSstatsPTMFormat | 0.063 | 0.002 | 0.065 | |
| PStoMSstatsPTMFormat | 0.040 | 0.001 | 0.041 | |
| ProgenesistoMSstatsPTMFormat | 0.042 | 0.001 | 0.043 | |
| SkylinetoMSstatsPTMFormat | 0.042 | 0.001 | 0.043 | |
| SpectronauttoMSstatsPTMFormat | 0.044 | 0.001 | 0.044 | |
| annotSite | 0.001 | 0.001 | 0.000 | |
| dataProcessPlotsPTM | 2.482 | 0.069 | 2.560 | |
| dataSummarizationPTM | 2.006 | 0.047 | 2.058 | |
| dataSummarizationPTM_TMT | 3.669 | 0.120 | 3.802 | |
| designSampleSizePTM | 4.049 | 0.053 | 4.113 | |
| groupComparisonPTM | 4.282 | 0.062 | 4.361 | |
| groupComparisonPlotsPTM | 11.213 | 0.101 | 11.410 | |
| locateMod | 0.001 | 0.000 | 0.001 | |
| locatePTM | 0.035 | 0.001 | 0.061 | |
| raw.input | 0.040 | 0.000 | 0.056 | |
| raw.input.tmt | 0.004 | 0.001 | 0.006 | |
| summary.data | 0.304 | 0.756 | 1.192 | |
| summary.data.tmt | 0.600 | 1.854 | 2.870 | |
| tidyFasta | 0.007 | 0.001 | 0.008 | |