Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:28 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 1611/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ptairMS 1.10.0 (landing page) camille Roquencourt
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the ptairMS 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: ptairMS |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.10.0.tar.gz |
StartedAt: 2024-03-27 23:06:03 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:15:27 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 563.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ptairMS.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ptairMS.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.10.0’ * 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 ‘ptairMS’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ptairMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... WARNING '::' or ':::' imports not declared from: ‘htmlwidgets’ ‘plyr’ There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’ ‘processFileTemporalNominalMass’ ‘tofToMz’ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed detectPeak 95.340 5.875 101.317 imputeMat 16.907 1.570 18.552 alignSamples 16.401 1.565 18.004 writeEset 15.897 1.590 17.514 impute 15.414 1.248 17.263 getPeakList 15.251 1.066 16.987 annotation 13.698 1.139 14.885 plot 12.577 1.161 13.754 plotTIC 12.021 1.097 13.141 plotFeatures 11.942 0.850 12.825 plotRaw 11.041 0.930 11.987 defineKnots 10.388 0.669 11.059 plotCalib 10.189 0.802 11.007 getSampleMetadata 10.115 0.670 11.063 setSampleMetadata 9.581 1.123 10.771 getDirectory 9.290 1.146 10.462 importSampleMetadata 9.464 0.667 10.306 resetSampleMetadata 9.520 0.548 10.095 rmPeakList 9.481 0.530 10.013 getFileNames 9.277 0.631 9.921 exportSampleMetada 9.184 0.699 9.969 changeTimeLimits 8.921 0.821 9.757 updatePtrSet 8.990 0.654 9.644 createPtrSet 7.489 0.656 8.174 convert_to_mzML 7.706 0.300 8.005 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. └─ptairMS (local) test_alignSamples() 2. └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 1) at test-alignment.R:40:3 ── Failure ('test-annotation.R:32:1'): annotateVOC function and findIsotope ──── Biobase::fData(bacteria.eset)[1, "isotope"] not equal to row.names(Biobase::fData(bacteria.eset))[2]. 1/1 mismatches x[1]: "60.0514" y[1]: "59.0608" Backtrace: ▆ 1. └─ptairMS (local) test_annotateVOC_and_isotope() 2. └─testthat::expect_equal(...) at test-annotation.R:28:3 [ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ] Error: Test failures Execution halted * 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 ERROR, 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ptairMS.Rcheck/00check.log’ for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align.cpp -o align.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findEqualGreaterM.cpp -o findEqualGreaterM.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-ptairMS/00new/ptairMS/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ ** testing if installed package keeps a record of temporary installation path * DONE (ptairMS)
ptairMS.Rcheck/tests/testthat.Rout.fail
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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. > library(testthat) > library(ptairMS) Warning message: replacing previous import 'Biobase::cache' by 'bit64::cache' when loading 'ptairMS' > > test_check("ptairMS") Control1.h5 : 3 peaks detected Control2.h5 : 4 peaks detected Specie-a1.h5 : 2 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 4 peaks detected specie-b2.h5 : 3 peaks detected Control1.h5 : 2 peaks detected Control2.h5 : 2 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 2 peaks detected specie-b2.h5 : 3 peaks detected Control1.h5 : 4 peaks detected Control2.h5 : 6 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 4 peaks detected specie-b1.h5 : 5 peaks detected specie-b2.h5 : 4 peaks detected Control1.h5 : 3 peaks detected Control2.h5 : 2 peaks detected Specie-a1.h5 : 3 peaks detected Specie-a2.h5 : 3 peaks detected specie-b1.h5 : 4 peaks detected specie-b2.h5 : 4 peaks detected [ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-alignment.R:59:1'): alignSamples() works correctly. ────────── nrow(Biobase::exprs(eset)) not equal to 2. 1/1 mismatches [1] 3 - 2 == 1 Backtrace: ▆ 1. └─ptairMS (local) test_alignSamples() 2. └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 2) at test-alignment.R:34:3 ── Failure ('test-alignment.R:59:1'): alignSamples() works correctly. ────────── nrow(Biobase::exprs(eset)) not equal to 1. 1/1 mismatches [1] 2 - 1 == 1 Backtrace: ▆ 1. └─ptairMS (local) test_alignSamples() 2. └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 1) at test-alignment.R:40:3 ── Failure ('test-annotation.R:32:1'): annotateVOC function and findIsotope ──── Biobase::fData(bacteria.eset)[1, "isotope"] not equal to row.names(Biobase::fData(bacteria.eset))[2]. 1/1 mismatches x[1]: "60.0514" y[1]: "59.0608" Backtrace: ▆ 1. └─ptairMS (local) test_annotateVOC_and_isotope() 2. └─testthat::expect_equal(...) at test-annotation.R:28:3 [ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ] Error: Test failures Execution halted
ptairMS.Rcheck/ptairMS-Ex.timings
name | user | system | elapsed | |
LocalMaximaSG | 0.038 | 0.005 | 0.042 | |
PeakList | 0.972 | 0.121 | 1.098 | |
RunShinnyApp | 0 | 0 | 0 | |
alignSamples | 16.401 | 1.565 | 18.004 | |
annotation | 13.698 | 1.139 | 14.885 | |
calibration | 0.767 | 0.139 | 0.906 | |
changeTimeLimits | 8.921 | 0.821 | 9.757 | |
convert_to_mzML | 7.706 | 0.300 | 8.005 | |
createPtrSet | 7.489 | 0.656 | 8.174 | |
defineKnots | 10.388 | 0.669 | 11.059 | |
detectPeak | 95.340 | 5.875 | 101.317 | |
exportSampleMetada | 9.184 | 0.699 | 9.969 | |
formula2mass | 0.004 | 0.001 | 0.005 | |
getDirectory | 9.290 | 1.146 | 10.462 | |
getFileNames | 9.277 | 0.631 | 9.921 | |
getPeakList | 15.251 | 1.066 | 16.987 | |
getSampleMetadata | 10.115 | 0.670 | 11.063 | |
importSampleMetadata | 9.464 | 0.667 | 10.306 | |
impute | 15.414 | 1.248 | 17.263 | |
imputeMat | 16.907 | 1.570 | 18.552 | |
plot | 12.577 | 1.161 | 13.754 | |
plotCalib | 10.189 | 0.802 | 11.007 | |
plotFeatures | 11.942 | 0.850 | 12.825 | |
plotRaw | 11.041 | 0.930 | 11.987 | |
plotTIC | 12.021 | 1.097 | 13.141 | |
readRaw | 0.146 | 0.037 | 0.184 | |
resetSampleMetadata | 9.520 | 0.548 | 10.095 | |
rmPeakList | 9.481 | 0.530 | 10.013 | |
setSampleMetadata | 9.581 | 1.123 | 10.771 | |
timeLimits | 1.564 | 0.096 | 1.662 | |
updatePtrSet | 8.990 | 0.654 | 9.644 | |
writeEset | 15.897 | 1.590 | 17.514 | |