| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-03 02:36:10 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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 1280/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsShiny 1.1.7 (landing page) Devon Kohler
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: MSstatsShiny |
| Version: 1.1.7 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSstatsShiny_1.1.7.tar.gz |
| StartedAt: 2023-02-02 13:50:13 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 13:54:28 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 254.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsShiny.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSstatsShiny_1.1.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSstatsShiny.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsShiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsShiny’ version ‘1.1.7’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tmt_model 9.567 0.080 9.605
tmt_summarization_loop 7.207 0.060 7.275
apply_adj 6.287 0.112 6.402
lf_summarization_loop 5.012 0.261 5.280
* 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 ...
‘MSstatsShiny_Launch_Instructions.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MSstatsShiny.Rcheck/00check.log’
for details.
MSstatsShiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MSstatsShiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 [2023-02-02 13:53:42] ** Raw data from Skyline imported successfully.
INFO [2023-02-02 13:53:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-02-02 13:53:43] ** Using provided annotation.
INFO [2023-02-02 13:53:43] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-02-02 13:53:43] ** 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 [2023-02-02 13:53:43] ** Rows with values of StandardType equal to iRT are removed
INFO [2023-02-02 13:53:43] ** Intensities with values of Truncated equal to TRUE are replaced with NA
INFO [2023-02-02 13:53:43] ** Intensities with values not smaller than 0.01 in DetectionQValue are replaced with 0
INFO [2023-02-02 13:53:43] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-02-02 13:53:43] ** Features with all missing measurements across runs are removed.
INFO [2023-02-02 13:53:43] ** Shared peptides are removed.
INFO [2023-02-02 13:53:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-02-02 13:53:44] ** Features with one or two measurements across runs are removed.
INFO [2023-02-02 13:53:44] Proteins with a single feature are removed.
INFO [2023-02-02 13:53:44] ** Run annotation merged with quantification data.
INFO [2023-02-02 13:53:44] ** Features with one or two measurements across runs are removed.
INFO [2023-02-02 13:53:44] ** Fractionation handled.
INFO [2023-02-02 13:53:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-02-02 13:53:44] ** 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 [2023-02-02 13:53:45] ** There are 22069 intensities which are zero or less than 1. These intensities are replaced with 1
INFO [2023-02-02 13:53:45] ** Log2 intensities under cutoff = -14.012 were considered as censored missing values.
INFO [2023-02-02 13:53:45] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:45] ** 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 [2023-02-02 13:53:48] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2023-02-02 13:53:48] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2023-02-02 13:53:48] ** Using provided annotation.
INFO [2023-02-02 13:53:48] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-02-02 13:53:48] ** 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 [2023-02-02 13:53:48] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-02-02 13:53:48] ** Shared peptides are removed.
INFO [2023-02-02 13:53:48] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-02-02 13:53:49] ** PSMs have been aggregated to peptide ions.
INFO [2023-02-02 13:53:50] ** Run annotation merged with quantification data.
INFO [2023-02-02 13:53:50] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-02-02 13:53:50] ** Fractionation handled.
INFO [2023-02-02 13:53:50] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-02-02 13:53:50] ** 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
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
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
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 INFO [2023-02-02 13:53:50] ** MSstatsTMT - proteinSummarization function
INFO [2023-02-02 13:53:50] ** Log2 intensities under cutoff = 9.0898 were considered as censored missing values.
INFO [2023-02-02 13:53:50] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:50] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:50] ** Log2 intensities under cutoff = 8.4416 were considered as censored missing values.
INFO [2023-02-02 13:53:50] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:50] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:51] ** Log2 intensities under cutoff = 9.8984 were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:51] ** Log2 intensities under cutoff = 8.7343 were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:51] ** Log2 intensities under cutoff = 7.1531 were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:51] ** Log2 intensities under cutoff = 7.0269 were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:51] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:52] ** Log2 intensities under cutoff = 8.3567 were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:52] ** Log2 intensities under cutoff = 8.4623 were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:52] ** Log2 intensities under cutoff = 9.4679 were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:52] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:53] ** Log2 intensities under cutoff = 9.6095 were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:53] ** Log2 intensities under cutoff = 7.0408 were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:53] ** Log2 intensities under cutoff = 9.8443 were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:53] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:54] ** Log2 intensities under cutoff = 8.7694 were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:54] ** Log2 intensities under cutoff = 9.7713 were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** Use all features that the dataset originally has.
INFO [2023-02-02 13:53:54] ** Log2 intensities under cutoff = 7.8583 were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-02-02 13:53:54] ** 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
test_backend_functionality.R.. 4 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 [2023-02-02 13:53:55] Design: 5 mixtures.
INFO [2023-02-02 13:53:55] Design: 3 technical replicated MS runs per mixture.
INFO [2023-02-02 13:53:55] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-02-02 13:53:55] Model fitting for 10 proteins.
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test_backend_functionality.R.. 6 tests [0;32mOK[0m Starting PTM modeling...
INFO [2023-02-02 13:53:58] == Start to test and get inference in whole plot ...
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INFO [2023-02-02 13:54:03] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2023-02-02 13:54:03] == Start to test and get inference in whole plot ...
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INFO [2023-02-02 13:54:04] == Comparisons for all proteins are done.
Starting adjustment...
test_backend_functionality.R.. 6 tests [0;32mOK[0m
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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;34m22.9s[0m
All ok, 23 results (22.9s)
Warning message:
In eval(jsub, SDenv, parent.frame()) : NAs introduced by coercion
>
> proc.time()
user system elapsed
30.038 0.452 30.920
MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings
| name | user | system | elapsed | |
| QC_check | 0.000 | 0.000 | 0.001 | |
| apply_adj | 6.287 | 0.112 | 6.402 | |
| dia_skyline_model | 0.031 | 0.019 | 0.051 | |
| dia_skyline_summarized | 0.344 | 0.200 | 0.545 | |
| example_dia_skyline | 0.220 | 0.004 | 0.225 | |
| example_skyline_annotation | 0.003 | 0.000 | 0.003 | |
| groupComparisonPlots2 | 0.956 | 0.003 | 0.963 | |
| launch_MSstatsShiny | 0.001 | 0.000 | 0.001 | |
| lf_model | 0.275 | 0.004 | 0.279 | |
| lf_summarization_loop | 5.012 | 0.261 | 5.280 | |
| radioTooltip | 0.005 | 0.000 | 0.005 | |
| tmt_model | 9.567 | 0.080 | 9.605 | |
| tmt_pd_model | 0.104 | 0.004 | 0.108 | |
| tmt_pd_summarized | 0.420 | 0.212 | 0.633 | |
| tmt_summarization_loop | 7.207 | 0.060 | 7.275 | |
| xy_str | 0 | 0 | 0 | |