Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2075/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Streamer 1.52.0 (landing page) Martin Morgan
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the Streamer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Streamer.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: Streamer |
Version: 1.52.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Streamer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Streamer_1.52.0.tar.gz |
StartedAt: 2024-12-20 10:24:24 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:25:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 74.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Streamer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Streamer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Streamer_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Streamer.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Streamer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Streamer’ version ‘1.52.0’ * 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 ‘Streamer’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘parallel:::mckill’ ‘parallel:::sendMaster’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘unit_tests.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Streamer.Rcheck/00check.log’ for details.
Streamer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Streamer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Streamer’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Streamer.c -o R_init_Streamer.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c raw_input.c -o raw_input.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Streamer.so R_init_Streamer.o raw_input.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-Streamer/00new/Streamer/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Streamer)
Streamer.Rcheck/tests/unit_tests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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("Streamer") Timing stopped at: 0.001 0 0 Error in DEACTIVATED("should error with only a consumer (?)") : should error with only a consumer (?) In addition: Warning messages: 1: In for (a in as.list(elist)) if (!missing(a) && mayCallBrowser(a, : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Streamer/extdata/s_1_sequence.txt) 2: In for (a in as.list(elist)) if (!missing(a) && mayCallBrowser(a, : closing unused connection 3 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Streamer/extdata/s_1_sequence.txt) RUNIT TEST PROTOCOL -- Fri Dec 20 10:25:24 2024 *********************************************** Number of test functions: 14 Number of deactivated test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : Streamer RUnit Tests - 14 test functions, 0 errors, 0 failures Number of test functions: 14 Number of deactivated test functions: 1 Number of errors: 0 Number of failures: 0 Warning message: In for (field in fields) { : closing unused connection 3 (/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Streamer/extdata/s_1_sequence.txt) > > proc.time() user system elapsed 2.591 0.646 3.034
Streamer.Rcheck/Streamer-Ex.timings
name | user | system | elapsed | |
ConnectionProducer-classes | 0.356 | 0.028 | 0.395 | |
Consumer-class | 0.003 | 0.001 | 0.004 | |
DAGTeam-class | 0.510 | 0.035 | 0.552 | |
Downsample-class | 0.002 | 0.001 | 0.002 | |
FunctionProducerConsumer-classes | 1.074 | 0.004 | 1.090 | |
ParallelParam-classes | 0.006 | 0.001 | 0.007 | |
Producer-class | 0.045 | 0.002 | 0.047 | |
RawInput-class | 0.016 | 0.004 | 0.022 | |
Reducer-class | 1.228 | 0.272 | 1.412 | |
Seq-class | 0.010 | 0.002 | 0.012 | |
Stream-class | 0.098 | 0.011 | 0.110 | |
Streamer-package | 0.109 | 0.010 | 0.121 | |
Team-class | 2.166 | 0.431 | 2.506 | |
Utility-classes | 0.002 | 0.002 | 0.003 | |
reset | 0 | 0 | 0 | |
status | 0 | 0 | 0 | |
yield | 0.000 | 0.000 | 0.001 | |