Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1037/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IRanges 2.39.2 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the IRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRanges.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: IRanges |
Version: 2.39.2 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IRanges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IRanges_2.39.2.tar.gz |
StartedAt: 2024-08-21 01:55:50 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:59:36 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 226.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IRanges.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IRanges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IRanges_2.39.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/IRanges.Rcheck' * using R version 4.4.1 (2024-06-14 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 'IRanges/DESCRIPTION' ... OK * this is package 'IRanges' version '2.39.2' * 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 'IRanges' can be installed ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE setCompressedListSummaryMethod : <anonymous>: no visible binding for global variable 'C_fun' setCompressedListWhichSummaryMethod : def: no visible binding for global variable 'C_fun' Undefined global functions or variables: C_fun * checking Rd files ... NOTE checkRd: (-1) nearest-methods.Rd:69-87: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:88-93: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:94-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:100-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:140-143: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:144-148: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'IntegerRangesList-class.Rd': '[IRanges]{RangesList}' Missing link or links in Rd file 'intra-range-methods.Rd': 'RangesList' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: '%poutside%' '%pover%' '%pwithin%' 'cvg' 'heads' 'slidingIRanges' 'slidingViews' 'tails' 'windows' Undocumented S4 classes: 'BaseManyToManyGrouping' 'Pos' 'CompressedIntegerRangesList' 'IPosList' 'CompressedRangesList' 'SimpleIPosList' 'RangesList' 'CompressedPosList' 'CompressedIPosList' 'Ranges' 'SimplePosList' 'PosList' 'SimpleRangesList' Undocumented S4 methods: generic 'anyDuplicated' and siglist 'RangesNSBS' generic 'as.factor' and siglist 'ManyToOneGrouping' generic 'as.integer' and siglist 'NormalIRanges' generic 'as.integer' and siglist 'Pos' generic 'as.integer' and siglist 'RangesNSBS' generic 'cbind' and siglist 'Rle' generic 'cbind' and siglist 'RleList' generic 'chartr' and siglist 'ANY,ANY,CharacterList' generic 'chartr' and siglist 'ANY,ANY,RleList' generic 'coerce' and siglist 'ANY,IPosRanges' generic 'coerce' and siglist 'AtomicList,RleViews' generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList' generic 'coerce' and siglist 'IPosRanges,IntegerList' generic 'coerce' and siglist 'IRanges,IPosList' generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList' generic 'coerce' and siglist 'IntegerRanges,IPosList' generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap' generic 'coerce' and siglist 'factor,ManyToOneGrouping' generic 'commonColnames<-' and siglist 'SplitDataFrameList' generic 'cvg' and siglist 'IntegerRanges' generic 'cvg' and siglist 'IntegerRangesList' generic 'endsWith' and siglist 'CharacterList' generic 'endsWith' and siglist 'RleList' generic 'extractROWS' and siglist 'CompressedList,ANY' generic 'extractROWS' and siglist 'IPos,ANY' generic 'extractROWS' and siglist 'MaskCollection,ANY' generic 'extractROWS' and siglist 'NormalIRanges,ANY' generic 'extractROWS' and siglist 'Partitioning,ANY' generic 'extractROWS' and siglist 'Rle,RangesNSBS' generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS' generic 'getListElement' and siglist 'CompressedList' generic 'getListElement' and siglist 'CompressedNormalIRangesList' generic 'getListElement' and siglist 'H2LGrouping' generic 'getListElement' and siglist 'MaskCollection' generic 'getListElement' and siglist 'NCLists' generic 'getListElement' and siglist 'Partitioning' generic 'getListElement' and siglist 'Views' generic 'gsub' and siglist 'ANY,ANY,CharacterList' generic 'gsub' and siglist 'ANY,ANY,RleList' generic 'ifelse2' and siglist 'ANY,List,List' generic 'is.unsorted' and siglist 'CompressedIntegerList' generic 'is.unsorted' and siglist 'CompressedLogicalList' generic 'is.unsorted' and siglist 'CompressedNumericList' generic 'isNormal' and siglist 'IntegerRanges' generic 'length' and siglist 'RangesNSBS' generic 'nchar' and siglist 'CharacterList' generic 'nchar' and siglist 'RleList' generic 'pcompareRecursively' and siglist 'IPosRanges' generic 'range' and siglist 'CompressedRleList' generic 'relist' and siglist 'grouping,missing' generic 'replaceROWS' and siglist 'IRanges' generic 'replaceROWS' and siglist 'NormalIRanges' generic 'slidingWindows' and siglist 'IntegerRanges' generic 'startsWith' and siglist 'CharacterList' generic 'startsWith' and siglist 'RleList' generic 'sub' and siglist 'ANY,ANY,CharacterList' generic 'sub' and siglist 'ANY,ANY,RleList' generic 'tile' and siglist 'IntegerRanges' generic 'tolower' and siglist 'CharacterList' generic 'tolower' and siglist 'RleList' generic 'toupper' and siglist 'CharacterList' generic 'toupper' and siglist 'RleList' generic 'updateObject' and siglist 'CompressedList' generic 'updateObject' and siglist 'IPosRanges' generic 'whichFirstNotNormal' and siglist 'IntegerRanges' generic 'windows' and siglist 'list_OR_List' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in Rd file 'nearest-methods.Rd': 'hits' '...' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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-3.20-bioc/R/library/IRanges/libs/x64/IRanges.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 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 IPos-class 9.52 0.65 10.26 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.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: 3 WARNINGs, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/IRanges.Rcheck/00check.log' for details.
IRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL IRanges ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'IRanges' ... ** 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/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 CompressedList_class.c -o CompressedList_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 Grouping_class.c -o Grouping_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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_class.c -o IRanges_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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_constructor.c -o IRanges_constructor.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 NCList.c -o NCList.o NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function] 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function] 202 | static const NCList *next_top_down(const NCList *nclist) | ^~~~~~~~~~~~~ NCList.c: In function 'C_find_overlaps_in_groups_NCList': NCList.c:1608:24: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 1608 | return ans; | ^~~ NCList.c:1546:14: note: 'ans' was declared here 1546 | SEXP ans; | ^~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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_IRanges.c -o R_init_IRanges.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 Ranges_class.c -o Ranges_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 RleViews_utils.c -o RleViews_utils.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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/S4Vectors/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 coverage_methods.c -o coverage_methods.o In function 'shift_and_clip_ranges', inlined from 'compute_coverage_from_IRanges_holder' at coverage_methods.c:609:12: coverage_methods.c:579:35: warning: 'x_end' may be used uninitialized [-Wmaybe-uninitialized] 579 | if (*out_ranges_are_tiles && x_end != cvg_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c: In function 'compute_coverage_from_IRanges_holder': coverage_methods.c:495:28: note: 'x_end' was declared here 495 | i, j, x_start, x_end, shift_elt, tmp; | ^~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 extractListFragments.c -o extractListFragments.o extractListFragments.c: In function 'C_find_partition_overlaps': extractListFragments.c:85:25: warning: 'split_partitions_buf' may be used uninitialized [-Wmaybe-uninitialized] 85 | IntAE_insert_at(split_partitions_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | IntAE_get_nelt(split_partitions_buf), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | q_prev_end); | ~~~~~~~~~~~ extractListFragments.c:35:16: note: 'split_partitions_buf' was declared here 35 | IntAE *split_partitions_buf; | ^~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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 inter_range_methods.c -o inter_range_methods.o inter_range_methods.c: In function 'reduce_ranges.isra': inter_range_methods.c:156:35: warning: 'max_end' may be used uninitialized [-Wmaybe-uninitialized] 156 | width_inc = end_j - max_end; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ inter_range_methods.c:102:29: note: 'max_end' was declared here 102 | append_or_drop, max_end, gapwidth, delta, width_inc; | ^~~~~~~ inter_range_methods.c:165:33: warning: 'revmap_elt' may be used uninitialized [-Wmaybe-uninitialized] 165 | IntAE_insert_at(revmap_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 | IntAE_get_nelt(revmap_elt), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 167 | j + 1); | ~~~~~~ inter_range_methods.c:103:22: note: 'revmap_elt' was declared here 103 | IntAE *tmp, *revmap_elt; | ^~~~~~~~~~ inter_range_methods.c:154:39: warning: 'gapwidth' may be used uninitialized [-Wmaybe-uninitialized] 154 | delta += gapwidth; | ~~~~~~^~~~~~~~~~~ inter_range_methods.c:102:38: note: 'gapwidth' was declared here 102 | append_or_drop, max_end, gapwidth, delta, width_inc; | ^~~~~~~~ inter_range_methods.c:154:39: warning: 'delta' may be used uninitialized [-Wmaybe-uninitialized] 154 | delta += gapwidth; | ~~~~~~^~~~~~~~~~~ inter_range_methods.c:102:48: note: 'delta' was declared here 102 | append_or_drop, max_end, gapwidth, delta, width_inc; | ^~~~~ gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.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-IRanges/00new/IRanges/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'drop' from package 'base' in package 'IRanges' Creating a generic function for 'runmed' from package 'stats' in package 'IRanges' Creating a generic function for 'chartr' from package 'base' in package 'IRanges' Creating a generic function for 'toupper' from package 'base' in package 'IRanges' Creating a generic function for 'tolower' from package 'base' in package 'IRanges' Creating a generic function for 'sub' from package 'base' in package 'IRanges' Creating a generic function for 'gsub' from package 'base' in package 'IRanges' Creating a generic function for 'startsWith' from package 'base' in package 'IRanges' Creating a generic function for 'endsWith' from package 'base' in package 'IRanges' Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges' Creating a new generic function for 'windows' in package 'IRanges' ** 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 (IRanges)
IRanges.Rcheck/tests/run_unitTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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. > require("IRanges") || stop("unable to load IRanges package") Loading required package: IRanges 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 Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows [1] TRUE > IRanges:::.test() RUNIT TEST PROTOCOL -- Wed Aug 21 01:59:20 2024 *********************************************** Number of test functions: 99 Number of errors: 0 Number of failures: 0 1 Test Suite : IRanges RUnit Tests - 99 test functions, 0 errors, 0 failures Number of test functions: 99 Number of errors: 0 Number of failures: 0 Warning messages: 1: In recycleListElements(e1, en) : Some element lengths are not multiples of their corresponding element length in e1 2: In x + y : longer object length is not a multiple of shorter object length 3: In recycleListElements(e1, en) : Some element lengths are not multiples of their corresponding element length in e1 4: In x + y : longer object length is not a multiple of shorter object length > > proc.time() user system elapsed 100.56 1.45 102.06
IRanges.Rcheck/IRanges-Ex.timings
name | user | system | elapsed | |
AtomicList-class | 0.30 | 0.02 | 0.32 | |
AtomicList-utils | 0.03 | 0.02 | 0.04 | |
CompressedList-class | 0.04 | 0.00 | 0.05 | |
DataFrameList-class | 0.13 | 0.00 | 0.12 | |
Grouping-class | 0.06 | 0.00 | 0.06 | |
Hits-class-leftovers | 0.06 | 0.00 | 0.07 | |
IPos-class | 9.52 | 0.65 | 10.26 | |
IPosRanges-class | 0.06 | 0.00 | 0.07 | |
IPosRanges-comparison | 0.06 | 0.02 | 0.07 | |
IRanges-class | 4.10 | 0.04 | 4.14 | |
IRanges-constructor | 0.07 | 0.00 | 0.08 | |
IRanges-utils | 3.55 | 0.07 | 3.64 | |
IRangesList-class | 0.06 | 0.00 | 0.07 | |
IntegerRangesList-class | 0.08 | 0.00 | 0.07 | |
MaskCollection-class | 0.10 | 0.01 | 0.11 | |
NCList-class | 0.03 | 0.00 | 0.03 | |
RangedSelection-class | 0.03 | 0.00 | 0.04 | |
Rle-class-leftovers | 0 | 0 | 0 | |
RleViews-class | 0.05 | 0.03 | 0.07 | |
RleViewsList-class | 0.06 | 0.00 | 0.07 | |
Views-class | 0.06 | 0.00 | 0.06 | |
ViewsList-class | 0 | 0 | 0 | |
coverage-methods | 0.27 | 0.03 | 0.30 | |
extractList | 0.11 | 0.00 | 0.11 | |
extractListFragments | 0.78 | 0.00 | 0.79 | |
findOverlaps-methods | 0.28 | 0.00 | 0.28 | |
inter-range-methods | 0.72 | 0.02 | 0.74 | |
intra-range-methods | 0.55 | 0.00 | 0.55 | |
multisplit | 0.03 | 0.00 | 0.03 | |
nearest-methods | 0.17 | 0.00 | 0.17 | |
range-squeezers | 0 | 0 | 0 | |
read.Mask | 0.05 | 0.00 | 0.05 | |
reverse-methods | 0.08 | 0.00 | 0.07 | |
setops-methods | 0.34 | 0.00 | 0.35 | |
slice-methods | 0.02 | 0.00 | 0.01 | |
view-summarization-methods | 0.01 | 0.00 | 0.02 | |