Devon Kohler
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MSstatsShiny |
| git_branch: RELEASE_3_16 |
| git_last_commit: 3cb9cb3 |
| git_last_commit_date: 2023-03-02 14:49:59 -0400 (Thu, 02 Mar 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 MSstatsShiny package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsShiny.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 1291/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsShiny 1.0.10 (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: MSstatsShiny |
| Version: 1.0.10 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsShiny_1.0.10.tar.gz |
| StartedAt: 2023-04-10 21:25:42 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:28:56 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 194.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsShiny.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsShiny_1.0.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstatsShiny.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 ‘MSstatsShiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsShiny’ version ‘1.0.10’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsShiny’ 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:
‘MSstatsTMT:::.logSum’ ‘MSstatsTMT:::.summarizeSimpleStat’
‘MSstatsTMT:::.summarizeTMP’
‘MSstatsTMT:::MSstatsFitComparisonModelsTMT’
‘MSstatsTMT:::MSstatsGroupComparisonOutputTMT’
‘MSstatsTMT:::MSstatsModerateTTest’
‘MSstatsTMT:::MSstatsNormalizeTMT’
‘MSstatsTMT:::MSstatsPrepareForGroupComparisonTMT’
‘MSstatsTMT:::MSstatsPrepareForSummarizationTMT’
‘MSstatsTMT:::MSstatsSummarizationOutputTMT’
‘MSstatsTMT:::MSstatsTestSingleProteinTMT’
‘MSstatsTMT:::getProcessedTMT’ ‘MSstatsTMT:::getSummarizedTMT’
‘shinyBS:::buildTooltipOrPopoverOptionsList’ ‘shinyBS:::shinyBSDep’
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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tmt_model 5.976 0.129 6.125
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstatsShiny.Rcheck/00check.log’
for details.
MSstatsShiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsShiny ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘MSstatsShiny’ ... ** using staged installation ** R ** data ** 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 (MSstatsShiny)
MSstatsShiny.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("MSstatsShiny")
+ }
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m INFO [2023-04-10 21:28:32] ** Raw data from Skyline imported successfully.
INFO [2023-04-10 21:28:33] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-10 21:28:33] ** Using provided annotation.
INFO [2023-04-10 21:28:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-04-10 21:28:33] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-04-10 21:28:33] ** Rows with values of StandardType equal to iRT are removed
INFO [2023-04-10 21:28:33] ** Intensities with values of Truncated equal to TRUE are replaced with NA
INFO [2023-04-10 21:28:33] ** Intensities with values not smaller than 0.01 in DetectionQValue are replaced with 0
INFO [2023-04-10 21:28:33] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-04-10 21:28:33] ** Features with all missing measurements across runs are removed.
INFO [2023-04-10 21:28:33] ** Shared peptides are removed.
INFO [2023-04-10 21:28:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-04-10 21:28:33] ** Features with one or two measurements across runs are removed.
INFO [2023-04-10 21:28:33] Proteins with a single feature are removed.
INFO [2023-04-10 21:28:33] ** Run annotation merged with quantification data.
INFO [2023-04-10 21:28:34] ** Features with one or two measurements across runs are removed.
INFO [2023-04-10 21:28:34] ** Fractionation handled.
INFO [2023-04-10 21:28:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-04-10 21:28:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 1 tests [0;32mOK[0m INFO [2023-04-10 21:28:34] ** There are 22069 intensities which are zero or less than 1. These intensities are replaced with 1
INFO [2023-04-10 21:28:34] ** Log2 intensities under cutoff = -14.012 were considered as censored missing values.
INFO [2023-04-10 21:28:34] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:34] ** Use all features that the dataset originally has.
test_backend_functionality.R.. 1 tests [0;32mOK[0m
test_backend_functionality.R.. 2 tests [0;32mOK[0m
test_backend_functionality.R.. 2 tests [0;32mOK[0m
test_backend_functionality.R.. 2 tests [0;32mOK[0m
test_backend_functionality.R.. 2 tests [0;32mOK[0m
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test_backend_functionality.R.. 2 tests [0;32mOK[0m
test_backend_functionality.R.. 2 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m INFO [2023-04-10 21:28:36] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2023-04-10 21:28:36] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2023-04-10 21:28:36] ** Using provided annotation.
INFO [2023-04-10 21:28:36] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-04-10 21:28:36] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2023-04-10 21:28:36] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-04-10 21:28:36] ** Shared peptides are removed.
INFO [2023-04-10 21:28:36] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-04-10 21:28:37] ** PSMs have been aggregated to peptide ions.
INFO [2023-04-10 21:28:37] ** Run annotation merged with quantification data.
INFO [2023-04-10 21:28:37] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-04-10 21:28:37] ** Fractionation handled.
INFO [2023-04-10 21:28:37] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-04-10 21:28:38] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
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test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
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test_backend_functionality.R.. 3 tests [0;32mOK[0m
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test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m INFO [2023-04-10 21:28:38] ** MSstatsTMT - proteinSummarization function
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 9.0898 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 8.4416 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 9.8984 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 8.7343 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 7.1531 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:38] ** Log2 intensities under cutoff = 7.0269 were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:38] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:39] ** Log2 intensities under cutoff = 8.3567 were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:39] ** Log2 intensities under cutoff = 8.4623 were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:39] ** Log2 intensities under cutoff = 9.4679 were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:39] ** Log2 intensities under cutoff = 9.6095 were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:39] ** Log2 intensities under cutoff = 7.0408 were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:39] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:40] ** Log2 intensities under cutoff = 9.8443 were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:40] ** Log2 intensities under cutoff = 8.7694 were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:40] ** Log2 intensities under cutoff = 9.7713 were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Use all features that the dataset originally has.
INFO [2023-04-10 21:28:40] ** Log2 intensities under cutoff = 7.8583 were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-10 21:28:40] ** Use all features that the dataset originally has.
test_backend_functionality.R.. 3 tests [0;32mOK[0m
test_backend_functionality.R.. 3 tests [0;32mOK[0m
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test_backend_functionality.R.. 4 tests [0;32mOK[0m
test_backend_functionality.R.. 4 tests [0;32mOK[0m INFO [2023-04-10 21:28:40] Design: 5 mixtures.
INFO [2023-04-10 21:28:40] Design: 3 technical replicated MS runs per mixture.
INFO [2023-04-10 21:28:40] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-04-10 21:28:40] Model fitting for 10 proteins.
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test_backend_functionality.R.. 6 tests [0;32mOK[0m Starting PTM modeling...
INFO [2023-04-10 21:28:42] == Start to test and get inference in whole plot ...
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INFO [2023-04-10 21:28:46] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2023-04-10 21:28:46] == Start to test and get inference in whole plot ...
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INFO [2023-04-10 21:28:46] == Comparisons for all proteins are done.
Starting adjustment...
test_backend_functionality.R.. 6 tests [0;32mOK[0m
test_backend_functionality.R.. 7 tests [0;32mOK[0m
test_backend_functionality.R.. 8 tests [0;32mOK[0m
test_backend_functionality.R.. 9 tests [0;32mOK[0m
test_backend_functionality.R.. 9 tests [0;32mOK[0m
test_backend_functionality.R.. 10 tests [0;32mOK[0m
test_backend_functionality.R.. 10 tests [0;32mOK[0m
test_backend_functionality.R.. 11 tests [0;32mOK[0m
test_backend_functionality.R.. 12 tests [0;32mOK[0m
test_backend_functionality.R.. 13 tests [0;32mOK[0m
test_backend_functionality.R.. 14 tests [0;32mOK[0m
test_backend_functionality.R.. 15 tests [0;32mOK[0m
test_backend_functionality.R.. 16 tests [0;32mOK[0m
test_backend_functionality.R.. 17 tests [0;32mOK[0m
test_backend_functionality.R.. 18 tests [0;32mOK[0m
test_backend_functionality.R.. 19 tests [0;32mOK[0m
test_backend_functionality.R.. 20 tests [0;32mOK[0m
test_backend_functionality.R.. 21 tests [0;32mOK[0m
test_backend_functionality.R.. 22 tests [0;32mOK[0m
test_backend_functionality.R.. 23 tests [0;32mOK[0m [0;34m14.5s[0m
All ok, 23 results (14.5s)
Warning message:
In eval(jsub, SDenv, parent.frame()) : NAs introduced by coercion
>
> proc.time()
user system elapsed
19.799 0.806 20.683
MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings
| name | user | system | elapsed | |
| QC_check | 0.001 | 0.001 | 0.000 | |
| apply_adj | 4.339 | 0.082 | 4.428 | |
| dia_skyline_model | 0.034 | 0.028 | 0.062 | |
| dia_skyline_summarized | 0.393 | 0.455 | 0.855 | |
| example_dia_skyline | 0.219 | 0.010 | 0.229 | |
| example_skyline_annotation | 0.002 | 0.001 | 0.003 | |
| groupComparisonPlots2 | 0.260 | 0.008 | 0.269 | |
| launch_MSstatsShiny | 0.001 | 0.000 | 0.001 | |
| lf_model | 0.185 | 0.004 | 0.189 | |
| lf_summarization_loop | 3.639 | 0.623 | 4.282 | |
| radioTooltip | 0.004 | 0.000 | 0.004 | |
| tmt_model | 5.976 | 0.129 | 6.125 | |
| tmt_pd_model | 0.069 | 0.005 | 0.074 | |
| tmt_pd_summarized | 0.553 | 0.671 | 1.233 | |
| tmt_summarization_loop | 4.096 | 0.121 | 4.228 | |
| xy_str | 0.000 | 0.001 | 0.000 | |