Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2033/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Structstrings 1.21.0 (landing page) Felix G.M. Ernst
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the Structstrings package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Structstrings.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: Structstrings |
Version: 1.21.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Structstrings.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Structstrings_1.21.0.tar.gz |
StartedAt: 2024-06-10 10:44:52 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 10:52:30 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 458.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Structstrings.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Structstrings.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Structstrings_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Structstrings/DESCRIPTION' ... OK * this is package 'Structstrings' version '1.21.0' * 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 whether package 'Structstrings' can be installed ... WARNING Found the following significant warnings: DotBracketDataFrame_class.c:40:29: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] DotBracketDataFrame_class.c:40:31: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] DotBracketDataFrame_class.c:52:25: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] DotBracketDataFrame_class.c:52:27: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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: 'Biostrings:::.XStringSet.show_frame_header' 'S4Vectors:::new_SimpleList_from_list' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/Structstrings/libs/x64/Structstrings.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed getBasePairing 5.37 0.09 5.48 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/Structstrings.Rcheck/00check.log' for details.
Structstrings.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Structstrings ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Structstrings' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DotBracketDataFrame_class.c -o DotBracketDataFrame_class.o DotBracketDataFrame_class.c: In function 'get_base_pairing_per_char_pair': DotBracketDataFrame_class.c:40:29: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] 40 | error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close); | ~^ ~~~~~~~~~~~~ | | | | char * int | %d DotBracketDataFrame_class.c:40:31: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 40 | error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close); | ~^ ~~~~~~~~~~~~~ | | | | char * int | %d DotBracketDataFrame_class.c:52:25: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] 52 | error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close); | ~^ ~~~~~~~~~~~~ | | | | char * int | %d DotBracketDataFrame_class.c:52:27: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 52 | error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close); | ~^ ~~~~~~~~~~~~~ | | | | char * int | %d gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_Structstrings.c -o R_init_Structstrings.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o Structstrings.dll tmp.def DotBracketDataFrame_class.o IRanges_stubs.o R_init_Structstrings.o S4Vectors_stubs.o utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Structstrings/00new/Structstrings/libs/x64 ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Structstrings)
Structstrings.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(Structstrings) Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Biostrings Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit > > test_check("Structstrings") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 174 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 174 ] > > proc.time() user system elapsed 95.29 11.26 106.70
Structstrings.Rcheck/Structstrings-Ex.timings
name | user | system | elapsed | |
DotBracketDataFrame | 1.25 | 0.28 | 1.56 | |
DotBracketString | 0.06 | 0.00 | 0.06 | |
DotBracketStringSet-io | 1.16 | 0.07 | 1.22 | |
LoopIndexList | 0.07 | 0.00 | 0.07 | |
Structstrings-internals | 2.21 | 0.06 | 2.27 | |
StructuredXStringSet | 0.04 | 0.00 | 0.05 | |
convertAnnotation | 0.04 | 0.00 | 0.03 | |
getBasePairing | 5.37 | 0.09 | 5.48 | |