Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4415 |
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 2152/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TransView 1.49.0 (landing page) Julius Muller
| 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 TransView package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView |
Version: 1.49.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TransView.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TransView_1.49.0.tar.gz |
StartedAt: 2024-08-27 01:04:43 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 01:05:25 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 41.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TransView.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TransView.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TransView_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TransView/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TransView’ version ‘1.49.0’ * 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 ‘TransView’ can be installed ... WARNING Found the following significant warnings: parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat] parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2 * 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 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .gene2window : <anonymous> : <anonymous>: no visible global function definition for ‘median’ .gene2window: no visible binding for global variable ‘approx’ .onAttach: no visible global function definition for ‘packageDescription’ .test: no visible global function definition for ‘defineTestSuite’ .test: no visible global function definition for ‘runTestSuite’ .test: no visible global function definition for ‘printTextProtocol’ annotatePeaks : <anonymous>: no visible global function definition for ‘median’ gtf2gr: no visible global function definition for ‘read.table’ gtf2gr: no visible global function definition for ‘ave’ macs2gr: no visible global function definition for ‘read.delim’ meltPeak: no visible global function definition for ‘approx’ meltPeak: no visible global function definition for ‘lowess’ plotTV: no visible global function definition for ‘quantile’ plotTV: no visible global function definition for ‘kmeans’ plotTV: no visible global function definition for ‘as.dendrogram’ plotTV: no visible global function definition for ‘hclust’ plotTV: no visible global function definition for ‘as.dist’ plotTV: no visible global function definition for ‘dist’ plotTV: no visible global function definition for ‘order.dendrogram’ plotTV: no visible global function definition for ‘par’ plotTV: no visible global function definition for ‘layout’ plotTV: no visible global function definition for ‘image’ plotTV: no visible global function definition for ‘hist’ plotTV: no visible global function definition for ‘title’ plotTV: no visible global function definition for ‘mtext’ plotTV: no visible global function definition for ‘lines’ plotTV: no visible global function definition for ‘axis’ plotTV: no visible global function definition for ‘rainbow’ plotTV: no visible global function definition for ‘text’ plotTV: no visible global function definition for ‘rgb’ plotTV: no visible global function definition for ‘plot.new’ setTV: no visible global function definition for ‘object.size’ .setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical: no visible global function definition for ‘object.size’ Undefined global functions or variables: approx as.dendrogram as.dist ave axis defineTestSuite dist hclust hist image kmeans layout lines lowess median mtext object.size order.dendrogram packageDescription par plot.new printTextProtocol quantile rainbow read.delim read.table rgb runTestSuite text title Consider adding importFrom("grDevices", "rainbow", "rgb") importFrom("graphics", "axis", "hist", "image", "layout", "lines", "mtext", "par", "plot.new", "text", "title") importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave", "dist", "hclust", "kmeans", "lowess", "median", "order.dendrogram", "quantile") importFrom("utils", "object.size", "packageDescription", "read.delim", "read.table") to your NAMESPACE file. * 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 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 ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TransView/libs/TransView.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘TransView_unit_tests.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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck/00check.log’ for details.
TransView.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TransView ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TransView’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_TransView.c -o R_init_TransView.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bin_density.c -o bin_density.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c construct_dc.c -o construct_dc.o In file included from construct_dc.c:23: In file included from ./parse_sam.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/sam.h:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts.h:36: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes] HTS_FORMAT(HTS_PRINTF_FMT, 3, 4); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT' #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first))) ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c parse_sam.c -o parse_sam.o parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); ~~ ^~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat] warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read)); ~~ ^~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:23:23: note: expanded from macro 'bam1_cigar' #define bam1_cigar(b) (bam_get_cigar((b))) ^~~~~~~~~~~~~~~~~~~~ parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] printf("Pos %d\n",current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND, ^~~~~~~~~~~~~~~~~~~~~~ parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat] current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c slice_dc.c -o slice_dc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c visuals.c -o visuals.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-TransView/00new/TransView/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 (TransView)
TransView.Rcheck/tests/TransView_unit_tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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("TransView") || stop("unable to load TransView package") Loading required package: TransView 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors 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 Loading required package: GenomeInfoDb Welcome to TransView version 1.49.0 Attaching package: 'TransView' The following object is masked from 'package:GenomicRanges': pos The following object is masked from 'package:IRanges': pos The following object is masked from 'package:BiocGenerics': pos [1] TRUE > TransView:::.test() Version 2.09+ detected 21 peaks matching 172 rows matching 2862 rows matching Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit RUNIT TEST PROTOCOL -- Tue Aug 27 01:05:21 2024 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : TransView RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 2.693 1.971 4.667
TransView.Rcheck/TransView-Ex.timings
name | user | system | elapsed | |
DensityContainer-class | 0.001 | 0.000 | 0.001 | |
TVResults-class | 0 | 0 | 0 | |
TransView-package | 0 | 0 | 0 | |
annotatePeaks | 0.468 | 0.010 | 0.479 | |
gtf2gr | 0.014 | 0.000 | 0.014 | |
macs2gr | 0.007 | 0.001 | 0.008 | |
meltPeak | 0.331 | 0.569 | 0.902 | |
parseReads | 0.085 | 0.379 | 0.464 | |
peak2tss | 0.194 | 0.001 | 0.196 | |
plotTV | 0.190 | 0.709 | 0.901 | |
plotTVData | 0.174 | 0.578 | 0.760 | |
rmTV | 0.191 | 0.349 | 0.541 | |
slice1 | 0.176 | 0.584 | 0.760 | |
slice1T | 0.265 | 0.010 | 0.275 | |