Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-01-31 11:09:54 -0500 (Tue, 31 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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

CHECK results for MSstatsShiny on lconway


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.

raw results

Package 1291/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsShiny 1.0.7  (landing page)
Devon Kohler
Snapshot Date: 2023-01-30 14:00:05 -0500 (Mon, 30 Jan 2023)
git_url: https://git.bioconductor.org/packages/MSstatsShiny
git_branch: RELEASE_3_16
git_last_commit: adf43d8
git_last_commit_date: 2023-01-17 20:32:16 -0500 (Tue, 17 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsShiny
Version: 1.0.7
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_1.0.7.tar.gz
StartedAt: 2023-01-30 21:37:02 -0500 (Mon, 30 Jan 2023)
EndedAt: 2023-01-30 21:40:14 -0500 (Mon, 30 Jan 2023)
EllapsedTime: 192.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsShiny.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MSstatsShiny.Rcheck’
* using R version 4.2.2 (2022-10-31)
* 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 ‘1.0.7’
* 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 5.829  0.162    6.03
* 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.



Installation output

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)

Tests output

MSstatsShiny.Rcheck/tests/tinytest.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
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("MSstatsShiny")
+ }

test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK INFO  [2023-01-30 21:39:52] ** Raw data from Skyline imported successfully.
INFO  [2023-01-30 21:39:52] ** Raw data from Skyline cleaned successfully.
INFO  [2023-01-30 21:39:52] ** Using provided annotation.
INFO  [2023-01-30 21:39:52] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-01-30 21:39:52] ** 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  [2023-01-30 21:39:52] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2023-01-30 21:39:52] ** Intensities with values of Truncated equal to TRUE are replaced with NA
INFO  [2023-01-30 21:39:52] ** Intensities with values not smaller than 0.01 in DetectionQValue are replaced with 0
INFO  [2023-01-30 21:39:52] ** Sequences containing DECOY, Decoys are removed.
INFO  [2023-01-30 21:39:52] ** Features with all missing measurements across runs are removed.
INFO  [2023-01-30 21:39:52] ** Shared peptides are removed.
INFO  [2023-01-30 21:39:52] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2023-01-30 21:39:52] ** Features with one or two measurements across runs are removed.
INFO  [2023-01-30 21:39:53] Proteins with a single feature are removed.
INFO  [2023-01-30 21:39:53] ** Run annotation merged with quantification data.
INFO  [2023-01-30 21:39:53] ** Features with one or two measurements across runs are removed.
INFO  [2023-01-30 21:39:53] ** Fractionation handled.
INFO  [2023-01-30 21:39:53] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-01-30 21:39:53] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    1 tests OK INFO  [2023-01-30 21:39:53] ** There are 22069 intensities which are zero or less than 1. These intensities are replaced with 1
INFO  [2023-01-30 21:39:53] ** Log2 intensities under cutoff = -14.012  were considered as censored missing values.
INFO  [2023-01-30 21:39:53] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:53] ** Use all features that the dataset originally has.

test_backend_functionality.R..    1 tests OK 
test_backend_functionality.R..    2 tests OK 
test_backend_functionality.R..    2 tests OK 
test_backend_functionality.R..    2 tests OK 
test_backend_functionality.R..    2 tests OK 
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test_backend_functionality.R..    2 tests OK 
test_backend_functionality.R..    2 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK INFO  [2023-01-30 21:39:55] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2023-01-30 21:39:55] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2023-01-30 21:39:55] ** Using provided annotation.
INFO  [2023-01-30 21:39:55] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-01-30 21:39:55] ** 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  [2023-01-30 21:39:55] ** Features with all missing measurements across channels within each run are removed.
INFO  [2023-01-30 21:39:55] ** Shared peptides are removed.
INFO  [2023-01-30 21:39:55] ** Features with one or two measurements across channels within each run are removed.
INFO  [2023-01-30 21:39:57] ** PSMs have been aggregated to peptide ions.
INFO  [2023-01-30 21:39:57] ** Run annotation merged with quantification data.
INFO  [2023-01-30 21:39:57] ** Features with one or two measurements across channels within each run are removed.
INFO  [2023-01-30 21:39:57] ** Fractionation handled.
INFO  [2023-01-30 21:39:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-01-30 21:39:57] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK INFO  [2023-01-30 21:39:57] ** MSstatsTMT - proteinSummarization function
INFO  [2023-01-30 21:39:57] ** Log2 intensities under cutoff = 9.0898  were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:57] ** Log2 intensities under cutoff = 8.4416  were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:57] ** Log2 intensities under cutoff = 9.8984  were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:57] ** Log2 intensities under cutoff = 8.7343  were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:57] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 7.1531  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 7.0269  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 8.3567  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 8.4623  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 9.4679  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:58] ** Log2 intensities under cutoff = 9.6095  were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:58] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:59] ** Log2 intensities under cutoff = 7.0408  were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:59] ** Log2 intensities under cutoff = 9.8443  were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:59] ** Log2 intensities under cutoff = 8.7694  were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:59] ** Log2 intensities under cutoff = 9.7713  were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Use all features that the dataset originally has.
INFO  [2023-01-30 21:39:59] ** Log2 intensities under cutoff = 7.8583  were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2023-01-30 21:39:59] ** Use all features that the dataset originally has.

test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    3 tests OK 
test_backend_functionality.R..    4 tests OK 
test_backend_functionality.R..    4 tests OK 
test_backend_functionality.R..    4 tests OK 
test_backend_functionality.R..    4 tests OK INFO  [2023-01-30 21:40:00] Design: 5 mixtures.
INFO  [2023-01-30 21:40:00] Design: 3 technical replicated MS runs per mixture.
INFO  [2023-01-30 21:40:00] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2023-01-30 21:40:00] Model fitting for 10 proteins.

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test_backend_functionality.R..    4 tests OK 
test_backend_functionality.R..    4 tests OK 
test_backend_functionality.R..    5 tests OK 
test_backend_functionality.R..    6 tests OK Starting PTM modeling...
INFO  [2023-01-30 21:40:02]  == Start to test and get inference in whole plot ...

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INFO  [2023-01-30 21:40:05]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2023-01-30 21:40:05]  == Start to test and get inference in whole plot ...

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INFO  [2023-01-30 21:40:05]  == Comparisons for all proteins are done.
Starting adjustment...

test_backend_functionality.R..    6 tests OK 
test_backend_functionality.R..    7 tests OK 
test_backend_functionality.R..    8 tests OK 
test_backend_functionality.R..    9 tests OK 
test_backend_functionality.R..    9 tests OK 
test_backend_functionality.R..   10 tests OK 
test_backend_functionality.R..   10 tests OK 
test_backend_functionality.R..   11 tests OK 
test_backend_functionality.R..   12 tests OK 
test_backend_functionality.R..   13 tests OK 
test_backend_functionality.R..   14 tests OK 
test_backend_functionality.R..   15 tests OK 
test_backend_functionality.R..   16 tests OK 
test_backend_functionality.R..   17 tests OK 
test_backend_functionality.R..   18 tests OK 
test_backend_functionality.R..   19 tests OK 
test_backend_functionality.R..   20 tests OK 
test_backend_functionality.R..   21 tests OK 
test_backend_functionality.R..   22 tests OK 
test_backend_functionality.R..   23 tests OK 14.5s
All ok, 23 results (14.5s)
Warning message:
In eval(jsub, SDenv, parent.frame()) : NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
 20.153   0.828  21.131 

Example timings

MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings

nameusersystemelapsed
QC_check000
apply_adj4.6840.0944.807
dia_skyline_model0.0420.0350.078
dia_skyline_summarized0.4460.5030.954
example_dia_skyline0.5740.0140.589
example_skyline_annotation0.0020.0010.003
groupComparisonPlots20.2880.0080.297
launch_MSstatsShiny0.0010.0010.001
lf_model0.2090.0080.220
lf_summarization_loop2.6870.6373.344
radioTooltip0.0040.0000.004
tmt_model5.8290.1626.030
tmt_pd_model0.0820.0050.087
tmt_pd_summarized0.6350.5871.235
tmt_summarization_loop4.1560.1244.299
xy_str000