Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the GenomicTuples package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 781/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicTuples 1.33.0 (landing page) Peter Hickey
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: GenomicTuples |
Version: 1.33.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicTuples.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicTuples_1.33.0.tar.gz |
StartedAt: 2022-12-29 00:07:45 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 00:09:50 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 125.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicTuples.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicTuples.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicTuples_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicTuples.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GenomicTuples/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GenomicTuples' version '1.33.0' * 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 'GenomicTuples' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 12.2.0' * 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 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 Unexported objects imported by ':::' calls: 'GenomicRanges:::extraColumnSlotNames' 'GenomicRanges:::extraColumnSlots' 'GenomicRanges:::extraColumnSlotsAsDF' 'S4Vectors:::VH_recycle' 'S4Vectors:::orderBy' 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 ... WARNING checkRd: (5) GTuples-class.Rd:127-155: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:181-189: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:190-205: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:206-211: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:212-218: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:227-230: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:232-234: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:236-240: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:242-246: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:248-258: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:260-263: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:265-269: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:271-280: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:282-286: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:288-292: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:294-302: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:304-309: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:311-316: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:318-323: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:325-330: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:332-335: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:346-352: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:354-360: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:362-367: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:369-377: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:385-389: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:391-396: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:398-406: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:408-417: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:426-431: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:433-436: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:438-443: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:445-465: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:467-471: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:473-478: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:480-490: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:491-504: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:506-520: \item in \describe must have non-empty label checkRd: (5) GTuples-class.Rd:527-541: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:120-134: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:135-141: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:142-149: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:150-155: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:156-161: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:162-166: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:167-171: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:172-179: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:180-184: \item in \describe must have non-empty label checkRd: (5) GTuples-comparison.Rd:185-190: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:65-69: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:78-81: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:82-85: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:86-89: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:90-94: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:95-101: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:102-107: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:108-119: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:120-129: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:130-136: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:137-141: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:142-146: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:147-155: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:156-162: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:163-168: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:169-174: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:175-180: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:181-184: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:196-202: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:204-210: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:212-218: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:220-228: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:236-242: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:243-245: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:248-254: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:262-268: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:269-273: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:274-278: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:279-285: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:286-298: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:299-304: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:305-311: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:319-325: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:326-331: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:332-335: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:343-347: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:348-355: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:356-360: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:361-367: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:368-373: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:374-386: \item in \describe must have non-empty label checkRd: (5) GTuplesList-class.Rd:387-393: \item in \describe must have non-empty label * 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 for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/GenomicTuples/libs/x64/GenomicTuples.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (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 * 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, 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicTuples.Rcheck/00check.log' for details.
GenomicTuples.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomicTuples ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'GenomicTuples' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IPD.cpp -o IPD.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c allTuplesSorted.cpp -o allTuplesSorted.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pcompareGTuples.cpp -o pcompareGTuples.o g++ -std=gnu++11 -shared -s -static-libgcc -o GenomicTuples.dll tmp.def IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GenomicTuples/00new/GenomicTuples/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicTuples)
GenomicTuples.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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) > test_check("GenomicTuples") Loading required package: GenomicTuples Loading required package: GenomicRanges 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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: GenomeInfoDb [ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ] > > proc.time() user system elapsed 30.34 0.65 32.45
GenomicTuples.Rcheck/GenomicTuples-Ex.timings
name | user | system | elapsed | |
GTuples-class | 0.28 | 0.00 | 0.28 | |
GTuples-comparison | 0.33 | 0.00 | 0.32 | |
GTuplesList-class | 0.27 | 0.03 | 0.30 | |
findOverlaps-methods | 0.31 | 0.00 | 0.31 | |
illdefined-methods | 0.01 | 0.00 | 0.02 | |
intra-tuple-methods | 0.08 | 0.00 | 0.08 | |
nearest-methods | 0.44 | 0.00 | 0.44 | |
tuples-squeezers | 0 | 0 | 0 | |