Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -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 803/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicAlignments 1.41.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicAlignments package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.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: GenomicAlignments |
Version: 1.41.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicAlignments.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicAlignments_1.41.0.tar.gz |
StartedAt: 2024-06-10 03:07:44 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 03:17:29 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 585.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicAlignments.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicAlignments.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicAlignments_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicAlignments.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 'GenomicAlignments/DESCRIPTION' ... OK * this is package 'GenomicAlignments' version '1.41.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'GenomicAlignments' 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 ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Biostrings' 'Rsamtools' 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 ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.18.0 Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.16.0 Cannot process chunk/lines: The first version of GenomicAlignments was included in Bioconductor 2.14. Cannot process chunk/lines: The package was created from existing code in IRanges, ShortRead, Cannot process chunk/lines: Rsamtools and GenomicRanges. * 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 ... NOTE Unexported objects imported by ':::' calls: 'Rsamtools:::.BamViews_delegate' 'Rsamtools:::.findMateWithinGroups' 'Rsamtools:::.load_bamcols_from_scanBam_res' 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 ... NOTE checkRd: (-1) coordinate-mapping-methods.Rd:69-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:84-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:102-114: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:115-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) findSpliceOverlaps-methods.Rd:99-102: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:103-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) intra-range-methods.Rd:52-60: Lost braces 52 | \item(){ | ^ * 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-3.20-bioc/R/library/GenomicAlignments/libs/x64/GenomicAlignments.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 junctions-methods 15.25 3.61 20.33 readGAlignments 15.14 1.09 33.64 summarizeOverlaps-methods 9.74 1.80 125.20 sequenceLayer 8.61 1.56 10.17 coordinate-mapping-methods 7.13 1.53 8.86 findSpliceOverlaps-methods 4.84 0.56 5.42 * 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: 6 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicAlignments.Rcheck/00check.log' for details.
GenomicAlignments.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GenomicAlignments' ... ** 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'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/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/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/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'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cigar_utils.c -o cigar_utils.o In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from GenomicAlignments.h:1, from cigar_utils.c:1: In function 'make_CompressedIRangesList', inlined from 'cigar_ranges' at cigar_utils.c:680:2: cigar_utils.c:534:25: warning: 'range_buf1' may be used uninitialized [-Wmaybe-uninitialized] 534 | new_IRanges_from_IntPairAE("IRanges", range_buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:590:20: note: 'range_buf1' was declared here 590 | IntPairAE *range_buf1; | ^~~~~~~~~~ cigar_utils.c:674:37: warning: 'breakpoint' may be used uninitialized [-Wmaybe-uninitialized] 674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1); | ~~~~~~~~~~~^~~ cigar_utils.c:588:62: note: 'breakpoint' was declared here 588 | int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint, | ^~~~~~~~~~ cigar_utils.c:626:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized] 626 | if (*flag_elt == NA_INTEGER) { | ^~~~~~~~~ cigar_utils.c:593:20: note: 'flag_elt' was declared here 593 | const int *flag_elt, *pos_elt, *f_elt; | ^~~~~~~~ cigar_utils.c:656:29: warning: 'f_elt' may be used uninitialized [-Wmaybe-uninitialized] 656 | if (*f_elt == NA_INTEGER) | ^~~~~~ cigar_utils.c:593:41: note: 'f_elt' was declared here 593 | const int *flag_elt, *pos_elt, *f_elt; | ^~~~~ In function 'make_CompressedIRangesList', inlined from 'cigar_ranges' at cigar_utils.c:680:2: cigar_utils.c:542:25: warning: 'ans_breakpoints' may be used uninitialized [-Wmaybe-uninitialized] 542 | new_PartitioningByEnd("PartitioningByEnd", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 543 | breakpoints, NULL)); | ~~~~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:587:19: note: 'ans_breakpoints' was declared here 587 | SEXP ans, ans_breakpoints, f_levels, cigar_elt; | ^~~~~~~~~~~~~~~ cigar_utils.c: In function 'cigar_width': cigar_utils.c:708:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized] 708 | if (*flag_elt == NA_INTEGER) { | ^~~~~~~~~ cigar_utils.c:698:20: note: 'flag_elt' was declared here 698 | const int *flag_elt; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o coordinate_mapping_methods.c: In function 'to_ref': coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized] 219 | if (n == 0) | ^ coordinate_mapping_methods.c:172:7: note: 'n' was declared here 172 | int n, offset = 0, OPL, query_consumed = 0; | ^ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o In function 'unsafe_overlap_encoding', inlined from 'overlap_encoding' at encodeOverlaps_methods.c:209:2: encodeOverlaps_methods.c:182:9: warning: 'out_nelt0' may be used uninitialized [-Wmaybe-uninitialized] 182 | CharAE_delete_at(out, out_nelt0, j1 * nrow); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ encodeOverlaps_methods.c: In function 'overlap_encoding': encodeOverlaps_methods.c:99:13: note: 'out_nelt0' was declared here 99 | int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, | ^~~~~~~~~ gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_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-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)
GenomicAlignments.Rcheck/tests/run_unitTests.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. > require("GenomicAlignments") || stop("unable to load GenomicRanges package") Loading required package: GenomicAlignments 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 Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > GenomicAlignments:::.test() RUNIT TEST PROTOCOL -- Mon Jun 10 03:17:09 2024 *********************************************** Number of test functions: 42 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicAlignments RUnit Tests - 42 test functions, 0 errors, 0 failures Number of test functions: 42 Number of errors: 0 Number of failures: 0 Warning message: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, : 4 alignments with ambiguous pairing were dumped. Use 'getDumpedAlignments()' to retrieve them from the dump environment. > > proc.time() user system elapsed 28.84 5.67 70.46
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
name | user | system | elapsed | |
GAlignmentPairs-class | 1.04 | 0.03 | 1.08 | |
GAlignments-class | 0.45 | 0.00 | 0.46 | |
GAlignmentsList-class | 2.89 | 0.05 | 3.02 | |
GappedReads-class | 0.09 | 0.00 | 0.09 | |
OverlapEncodings-class | 1.05 | 0.12 | 1.19 | |
cigar-utils | 0.20 | 0.02 | 0.22 | |
coordinate-mapping-methods | 7.13 | 1.53 | 8.86 | |
coverage-methods | 2.99 | 0.09 | 3.08 | |
encodeOverlaps-methods | 0.03 | 0.00 | 0.03 | |
findCompatibleOverlaps-methods | 0.80 | 0.28 | 1.10 | |
findMateAlignment | 0.15 | 0.00 | 0.15 | |
findOverlaps-methods | 0.49 | 0.03 | 0.52 | |
findSpliceOverlaps-methods | 4.84 | 0.56 | 5.42 | |
intra-range-methods | 0.27 | 0.02 | 0.28 | |
junctions-methods | 15.25 | 3.61 | 20.33 | |
pileLettersAt | 0.79 | 0.00 | 0.81 | |
readGAlignments | 15.14 | 1.09 | 33.64 | |
sequenceLayer | 8.61 | 1.56 | 10.17 | |
setops-methods | 0.11 | 0.02 | 0.13 | |
stackStringsFromGAlignments | 4.19 | 0.31 | 4.50 | |
summarizeOverlaps-methods | 9.74 | 1.80 | 125.20 | |