| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1311/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsShiny 1.1.10 (landing page) Devon Kohler
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: MSstatsShiny |
| Version: 1.1.10 |
| 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/site-library --timings MSstatsShiny_1.1.10.tar.gz |
| StartedAt: 2023-04-12 07:45:06 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 07:48:55 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 228.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MSstatsShiny.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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/site-library --timings MSstatsShiny_1.1.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSstatsShiny.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsShiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsShiny’ version ‘1.1.10’
* 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 loading without being on the library search path ... 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 9.681 0.168 8.557
apply_adj 7.182 0.359 7.537
tmt_summarization_loop 7.048 0.159 5.987
* 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 ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘MSstatsShiny_Launch_Instructions.Rmd’ using rmarkdown
Error: processing vignette 'MSstatsShiny_Launch_Instructions.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘MSstatsShiny_Launch_Instructions.Rmd’
SUMMARY: processing the following file failed:
‘MSstatsShiny_Launch_Instructions.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 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/site-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) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2023-04-12 07:48:32] ** Raw data from Skyline imported successfully.
INFO [2023-04-12 07:48:33] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-12 07:48:33] ** Using provided annotation.
INFO [2023-04-12 07:48:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-04-12 07:48:33] ** 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 [2023-04-12 07:48:33] ** Rows with values of StandardType equal to iRT are removed
INFO [2023-04-12 07:48:33] ** Intensities with values of Truncated equal to TRUE are replaced with NA
INFO [2023-04-12 07:48:33] ** Intensities with values not smaller than 0.01 in DetectionQValue are replaced with 0
INFO [2023-04-12 07:48:33] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-04-12 07:48:33] ** Features with all missing measurements across runs are removed.
INFO [2023-04-12 07:48:33] ** Shared peptides are removed.
INFO [2023-04-12 07:48:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-04-12 07:48:34] ** Features with one or two measurements across runs are removed.
INFO [2023-04-12 07:48:34] Proteins with a single feature are removed.
INFO [2023-04-12 07:48:34] ** Run annotation merged with quantification data.
INFO [2023-04-12 07:48:34] ** Features with one or two measurements across runs are removed.
INFO [2023-04-12 07:48:34] ** Fractionation handled.
INFO [2023-04-12 07:48:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-04-12 07:48:34] ** 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 [2023-04-12 07:48:34] ** There are 22069 intensities which are zero or less than 1. These intensities are replaced with 1
INFO [2023-04-12 07:48:35] ** Log2 intensities under cutoff = -14.012 were considered as censored missing values.
INFO [2023-04-12 07:48:35] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:35] ** 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
|
| | 0%
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 [2023-04-12 07:48:36] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2023-04-12 07:48:37] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2023-04-12 07:48:37] ** Using provided annotation.
INFO [2023-04-12 07:48:37] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-04-12 07:48:37] ** 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 [2023-04-12 07:48:37] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-04-12 07:48:37] ** Shared peptides are removed.
INFO [2023-04-12 07:48:37] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-04-12 07:48:38] ** PSMs have been aggregated to peptide ions.
INFO [2023-04-12 07:48:38] ** Run annotation merged with quantification data.
INFO [2023-04-12 07:48:38] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-04-12 07:48:38] ** Fractionation handled.
INFO [2023-04-12 07:48:38] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-04-12 07:48:38] ** 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
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 [2023-04-12 07:48:38] ** MSstatsTMT - proteinSummarization function
INFO [2023-04-12 07:48:38] ** Log2 intensities under cutoff = 9.0898 were considered as censored missing values.
INFO [2023-04-12 07:48:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:38] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:38] ** Log2 intensities under cutoff = 8.4416 were considered as censored missing values.
INFO [2023-04-12 07:48:38] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:38] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:39] ** Log2 intensities under cutoff = 9.8984 were considered as censored missing values.
INFO [2023-04-12 07:48:39] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:39] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:40] ** Log2 intensities under cutoff = 8.7343 were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:40] ** Log2 intensities under cutoff = 7.1531 were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:40] ** Log2 intensities under cutoff = 7.0269 were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:40] ** Log2 intensities under cutoff = 8.3567 were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:40] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:41] ** Log2 intensities under cutoff = 8.4623 were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:41] ** Log2 intensities under cutoff = 9.4679 were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:41] ** Log2 intensities under cutoff = 9.6095 were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:41] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:42] ** Log2 intensities under cutoff = 7.0408 were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:42] ** Log2 intensities under cutoff = 9.8443 were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:42] ** Log2 intensities under cutoff = 8.7694 were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:42] ** Log2 intensities under cutoff = 9.7713 were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Use all features that the dataset originally has.
INFO [2023-04-12 07:48:42] ** Log2 intensities under cutoff = 7.8583 were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** Log2 intensities = NA were considered as censored missing values.
INFO [2023-04-12 07:48:42] ** 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
test_backend_functionality.R.. 4 tests [0;32mOK[0m
test_backend_functionality.R.. 4 tests [0;32mOK[0m
test_backend_functionality.R.. 4 tests [0;32mOK[0m INFO [2023-04-12 07:48:43] Design: 5 mixtures.
INFO [2023-04-12 07:48:43] Design: 3 technical replicated MS runs per mixture.
INFO [2023-04-12 07:48:43] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-04-12 07:48:43] Model fitting for 10 proteins.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
test_backend_functionality.R.. 4 tests [0;32mOK[0m
test_backend_functionality.R.. 4 tests [0;32mOK[0m
test_backend_functionality.R.. 5 tests [0;32mOK[0m
test_backend_functionality.R.. 6 tests [0;32mOK[0m Starting PTM modeling...
INFO [2023-04-12 07:48:44] == Start to test and get inference in whole plot ...
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================= | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================= | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================ | 69%
|
|================================================= | 70%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
INFO [2023-04-12 07:48:48] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2023-04-12 07:48:48] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=== | 4%
|
|===== | 8%
|
|======== | 12%
|
|=========== | 15%
|
|============= | 19%
|
|================ | 23%
|
|=================== | 27%
|
|====================== | 31%
|
|======================== | 35%
|
|=========================== | 38%
|
|============================== | 42%
|
|================================ | 46%
|
|=================================== | 50%
|
|====================================== | 54%
|
|======================================== | 58%
|
|=========================================== | 62%
|
|============================================== | 65%
|
|================================================ | 69%
|
|=================================================== | 73%
|
|====================================================== | 77%
|
|========================================================= | 81%
|
|=========================================================== | 85%
|
|============================================================== | 88%
|
|================================================================= | 92%
|
|=================================================================== | 96%
|
|======================================================================| 100%
INFO [2023-04-12 07:48:49] == 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;34m17.2s[0m
All ok, 23 results (17.2s)
Warning message:
In eval(jsub, SDenv, parent.frame()) : NAs introduced by coercion
>
> proc.time()
user system elapsed
25.544 0.815 24.471
MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings
| name | user | system | elapsed | |
| QC_check | 0.001 | 0.000 | 0.000 | |
| apply_adj | 7.182 | 0.359 | 7.537 | |
| dia_skyline_model | 0.046 | 0.000 | 0.047 | |
| dia_skyline_summarized | 0.428 | 0.251 | 0.679 | |
| example_dia_skyline | 0.285 | 0.039 | 0.326 | |
| example_skyline_annotation | 0.004 | 0.001 | 0.004 | |
| groupComparisonPlots2 | 1.280 | 0.075 | 1.356 | |
| launch_MSstatsShiny | 0.001 | 0.000 | 0.001 | |
| lf_model | 0.258 | 0.000 | 0.258 | |
| lf_summarization_loop | 3.982 | 0.195 | 3.467 | |
| radioTooltip | 0.006 | 0.000 | 0.005 | |
| tmt_model | 9.681 | 0.168 | 8.557 | |
| tmt_pd_model | 0.095 | 0.004 | 0.099 | |
| tmt_pd_summarized | 0.394 | 0.196 | 0.590 | |
| tmt_summarization_loop | 7.048 | 0.159 | 5.987 | |
| xy_str | 0.000 | 0.000 | 0.001 | |