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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ncdfFlow package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ncdfFlow.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1251/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ncdfFlow 2.38.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ncdfFlow |
Version: 2.38.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ncdfFlow_2.38.0.tar.gz |
StartedAt: 2021-10-14 21:41:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:43:09 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 108.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ncdfFlow.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ncdfFlow_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ncdfFlow/DESCRIPTION’ ... OK * this is package ‘ncdfFlow’ version ‘2.38.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ncdfFlow’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: lib 3.5Mb libs 3.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘flowCore’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘BH’ ‘RcppArmadillo’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘flowCore:::check_channel_alias’ ‘flowCore:::guid’ ‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’ ‘flowCore:::update_channel_by_alias’ 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 ... NOTE ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs = matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]), keyword(x[[guid]])), env = e1): partial argument match of 'env' to 'envir' rbind2,ncdfFlowList-ANY : <anonymous> : <anonymous>: warning in assign(curSample, NA, env = indiceEnv): partial argument match of 'env' to 'envir' read.ncdfFlowSet: no visible global function definition for ‘mclapply’ Undefined global functions or variables: mclapply * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ncdfFlow/libs/ncdfFlow.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_rand_r’, possibly from ‘rand_r’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Indices 6.213 0.299 6.523 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 WARNING, 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ncdfFlow.Rcheck/00check.log’ for details.
ncdfFlow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ncdfFlow ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ncdfFlow’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bitOps.cpp -o bitOps.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hdfFlow.cpp -o hdfFlow.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c readFrame.cpp -o readFrame.o mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib" ar rs "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o ar: creating archive /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ncdfFlow/00new/ncdfFlow/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 (ncdfFlow)
ncdfFlow.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(ncdfFlow) Loading required package: flowCore Loading required package: RcppArmadillo Loading required package: BH > > test_check("ncdfFlow") ══ Skipped tests ═══════════════════════════════════════════════════════════════ • ###this will cause crashing error see #50 (2) • file.exists(filename) is not TRUE (1) [ FAIL 0 | WARN 6 | SKIP 3 | PASS 338 ] Warning message: In for (j in seq_along(x)) { : closing unused connection 4 (/tmp/RtmpsK0t7t/file1286619f2b514) > #devtools::test("~/rglab/workspace/ncdfFlow") > #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowSet_accessor.R") > #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowList.R") > > > proc.time() user system elapsed 15.420 0.881 16.293
ncdfFlow.Rcheck/ncdfFlow-Ex.timings
name | user | system | elapsed | |
Indices | 6.213 | 0.299 | 6.523 | |
as.flowSet | 1.415 | 0.036 | 1.452 | |
clone.ncdfFlowSet | 0.271 | 0.021 | 0.293 | |
extractFlowFrame | 1.199 | 0.033 | 1.233 | |
ncdfFlowList-class | 0.881 | 0.029 | 0.910 | |
ncdfFlowSet-constructor | 0.770 | 0.020 | 0.792 | |
ncfsApply-ncdfFlowSet-method | 0.904 | 0.029 | 0.935 | |
rbind2-method | 0.951 | 0.033 | 0.984 | |
read.ncdfFlowSet | 0.659 | 0.021 | 0.683 | |
replacement-method-for-ncdfFlowSet | 0.857 | 0.016 | 0.874 | |
save_ncfs | 0.000 | 0.001 | 0.001 | |
subset-methods | 0.796 | 0.023 | 0.819 | |
unlink-ncdfFlowSet-method | 0.843 | 0.014 | 0.857 | |