Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 |
Package 1978/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
specL 1.39.0 (landing page) Christian Panse
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the specL package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: specL |
Version: 1.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:specL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings specL_1.39.0.tar.gz |
StartedAt: 2024-05-20 03:48:32 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 03:49:27 -0400 (Mon, 20 May 2024) |
EllapsedTime: 54.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: specL.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:specL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings specL_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/specL.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘specL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘specL’ version ‘1.39.0’ * 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 ‘specL’ 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 code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .retentiontimePlotFile : <anonymous>: no visible global function definition for ‘head’ summary,specLSet : <anonymous>: no visible binding for global variable ‘iRTpeptides’ Undefined global functions or variables: head iRTpeptides Consider adding importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc-mac-arm64/meat/specL.Rcheck/00check.log’ for details.
specL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL specL ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘specL’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (specL)
specL.Rcheck/tests/runTests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > BiocGenerics:::testPackage("specL") Attaching package: 'specL' The following objects are masked from 'package:protViz': plot.psm, plot.psmSet, summary.psmSet start protein annotation ... time taken: 0.000539902846018473 minutes start protein annotation ... time taken: 0.000382586320241292 minutes normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.267295122146606 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.241899013519287 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.187426090240479 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... no iRT peptides found for building the model. => no iRT regression applied, using orgiginal rt instead! generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.241235017776489 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0174481868743896 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0195980072021484 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.193866968154907 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... no iRT peptides found for building the model. => no iRT regression applied, using orgiginal rt instead! generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.243350982666016 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0198471546173096 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0202970504760742 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 69 length of genSwathIonLibSpecL 69 time taken: 0.128849029541016 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 69 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 68 length of genSwathIonLibSpecL 68 time taken: 0.138148069381714 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 68 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.253531932830811 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 69 length of genSwathIonLibSpecL 69 time taken: 0.127724885940552 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 69 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 68 length of genSwathIonLibSpecL 68 time taken: 0.135835886001587 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 68 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.223535060882568 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 fetched 137 rows. assigning 28 modifications ... fetched 184 rows. assigning 37 modifications ... normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.183847188949585 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 fetched 137 rows. assigning 28 modifications ... fetched 184 rows. assigning 37 modifications ... normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.202114105224609 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 RUNIT TEST PROTOCOL -- Mon May 20 03:49:17 2024 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : specL RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > > proc.time() user system elapsed 5.284 0.368 5.716
specL.Rcheck/specL-Ex.timings
name | user | system | elapsed | |
annotate.protein_id | 0.028 | 0.013 | 0.048 | |
cdsw | 0.017 | 0.003 | 0.019 | |
genSwathIonLib | 0.371 | 0.018 | 0.395 | |
iRTpeptides | 0.005 | 0.001 | 0.006 | |
peptideStd | 0.007 | 0.002 | 0.010 | |
read.bibliospec | 0.001 | 0.000 | 0.001 | |
specL-class | 0.001 | 0.001 | 0.001 | |
specLSet-class | 0.001 | 0.001 | 0.002 | |