Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1389/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ncdfFlow 2.53.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the ncdfFlow package: - 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 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: ncdfFlow |
Version: 2.53.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ncdfFlow_2.53.0.tar.gz |
StartedAt: 2024-12-23 00:23:01 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 00:24:29 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 88.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ncdfFlow.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ncdfFlow_2.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ncdfFlow/DESCRIPTION’ ... OK * this is package ‘ncdfFlow’ version ‘2.53.0’ * 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 ‘ncdfFlow’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 8.3Mb sub-directories of 1Mb or more: libs 7.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Non-standard license specification: AGPL-3.0-only Standardizable: FALSE 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 loading without being on the library search path ... 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. Package in Depends field not imported from: ‘BH’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * 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 ... NOTE checkRd: (-1) subset-functions.Rd:20: Lost braces 20 | a subset of code{ncdfFlowSet} or \code{ncdfFlowList} object | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: extractFlowFrame.Rd: [[,flowSet-method ncdfFlowSet-class.Rd: flowSet, Subset, exprs,flowFrame-method, phenoData,flowSet-method, flowSet-class ncdfFlowSet-split.Rd: split-methods ncfsApply-ncdfFlowSet-method.Rd: fsApply rbind2-method.Rd: rbind2,flowSet,flowSet-method read.ncdfFlowSet.Rd: read.FCS subset-methods.Rd: [,flowSet-method Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'extractFlowFrame.Rd': \S4method{[[}{ncdfFlowSet,ANY} Code: function(x, i, j, ...) Docs: function(x, i, j, use.exprs = TRUE, ...) Argument names in docs not in code: use.exprs Mismatches in argument names: Position: 4 Code: ... Docs: use.exprs * 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/ncdfFlow/libs/ncdfFlow.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘rand_r’, possibly from ‘rand_r’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.Rcheck/00check.log’ for details.
ncdfFlow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ncdfFlow ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ncdfFlow’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c hdfFlow.cpp -o hdfFlow.o hdfFlow.cpp: In function ‘void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<int>, int, int, double*, bool)’: hdfFlow.cpp:508:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 508 | if(sampleIndx >= nSample) | ~~~~~~~~~~~^~~~~~~~~~ hdfFlow.cpp:493:21: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 493 | herr_t status; | ^~~~~~ mkdir -p "/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib" ar rs "/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a" cpp11.o hdfFlow.o ar: creating /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so cpp11.o hdfFlow.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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: BH > > test_check("ncdfFlow") [ FAIL 0 | WARN 1 | SKIP 3 | PASS 335 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • ###this will cause crashing error see #50 (2): 'test_ncdfFlowSet_accessor.R:51:5', 'test_ncdfFlowSet_accessor.R:267:3' • file.exists(filename) is not TRUE (1): 'test_IO.R:6:3' [ FAIL 0 | WARN 1 | SKIP 3 | PASS 335 ] Warning message: In for (i in seq_len(n)) { : closing unused connection 4 (/tmp/RtmpEMlA9u/file1e5d9834850fc3) > #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 11.129 0.568 11.688
ncdfFlow.Rcheck/ncdfFlow-Ex.timings
name | user | system | elapsed | |
Indices | 4.482 | 0.286 | 4.767 | |
as.flowSet | 1.671 | 0.056 | 1.727 | |
clone.ncdfFlowSet | 0.183 | 0.012 | 0.195 | |
extractFlowFrame | 1.256 | 0.051 | 1.307 | |
ncdfFlowList-class | 1.301 | 0.035 | 1.337 | |
ncdfFlowSet-constructor | 1.611 | 0.067 | 1.678 | |
ncfsApply-ncdfFlowSet-method | 1.265 | 0.012 | 1.277 | |
rbind2-method | 1.291 | 0.045 | 1.336 | |
read.ncdfFlowSet | 0.176 | 0.015 | 0.191 | |
replacement-method-for-ncdfFlowSet | 1.262 | 0.009 | 1.271 | |
save_ncfs | 0 | 0 | 0 | |
subset-methods | 1.268 | 0.021 | 1.289 | |
unlink-ncdfFlowSet-method | 1.610 | 0.067 | 1.677 | |