| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:42 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1630/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ptairMS 1.12.0 (landing page) camille Roquencourt
| kjohnson3 | macOS 13.6.5 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-05-06 23:56:31 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-07 00:01:39 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 308.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ptairMS.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/ptairMS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.12.0’
* 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-3.19-bioc-mac-arm64/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 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 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 26.354 0.851 27.205
writeEset 5.361 0.316 5.679
getPeakList 4.745 0.345 5.092
* 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 ... 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-3.19-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/4.4-arm64/Resources/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.4-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/4.4-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/4.4-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/4.4-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 4.4.0 (2024-04-24) -- "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.
> 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 | 0.007 | 0.001 | 0.008 | |
| PeakList | 0.258 | 0.022 | 0.283 | |
| RunShinnyApp | 0 | 0 | 0 | |
| alignSamples | 4.325 | 0.309 | 4.647 | |
| annotation | 3.738 | 0.263 | 4.004 | |
| calibration | 0.246 | 0.026 | 0.273 | |
| changeTimeLimits | 2.373 | 0.172 | 2.546 | |
| convert_to_mzML | 3.891 | 0.119 | 4.007 | |
| createPtrSet | 2.319 | 0.031 | 2.362 | |
| defineKnots | 2.965 | 0.042 | 3.008 | |
| detectPeak | 26.354 | 0.851 | 27.205 | |
| exportSampleMetada | 2.730 | 0.113 | 2.843 | |
| formula2mass | 0.001 | 0.000 | 0.001 | |
| getDirectory | 2.570 | 0.242 | 2.813 | |
| getFileNames | 2.922 | 0.234 | 3.158 | |
| getPeakList | 4.745 | 0.345 | 5.092 | |
| getSampleMetadata | 2.409 | 0.052 | 2.462 | |
| importSampleMetadata | 2.674 | 0.052 | 2.728 | |
| impute | 3.931 | 0.106 | 4.038 | |
| imputeMat | 4.263 | 0.233 | 4.499 | |
| plot | 3.450 | 0.258 | 3.710 | |
| plotCalib | 3.050 | 0.246 | 3.296 | |
| plotFeatures | 2.762 | 0.215 | 2.982 | |
| plotRaw | 3.132 | 0.225 | 3.360 | |
| plotTIC | 3.218 | 0.225 | 3.444 | |
| readRaw | 0.044 | 0.007 | 0.050 | |
| resetSampleMetadata | 3.248 | 0.214 | 3.463 | |
| rmPeakList | 3.134 | 0.206 | 3.341 | |
| setSampleMetadata | 2.752 | 0.196 | 2.949 | |
| timeLimits | 0.278 | 0.020 | 0.298 | |
| updatePtrSet | 3.212 | 0.210 | 3.423 | |
| writeEset | 5.361 | 0.316 | 5.679 | |