| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| 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 33/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| csaw 1.36.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the csaw package: - 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: csaw |
| Version: 1.36.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings csaw_1.36.1.tar.gz |
| StartedAt: 2024-03-08 16:02:06 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 16:10:16 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 490.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: csaw.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings csaw_1.36.1.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/csaw.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.36.1’
* 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 ‘csaw’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.3Mb
sub-directories of 1Mb or more:
libs 9.6Mb
* 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 loading without being on the library search path ... 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 ... 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 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 ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library/csaw/libs/csaw.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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. 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
detailRanges 15.469 0.732 16.206
* 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 ...
‘csaw.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-R41/meat/csaw.Rcheck/00check.log’
for details.
csaw.Rcheck/00install.out
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL csaw
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c annotator.cpp -o annotator.o
annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
annotator.cpp:47:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
47 | while (counter < nolaps && query[counter]==curreg) {
| ~~~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’:
best_in_cluster.cpp:11:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
11 | if (nwin!=clustids.size() || nwin!=winweight.size()) {
| ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:42: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
11 | if (nwin!=clustids.size() || nwin!=winweight.size()) {
| ~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c intersector.cpp -o intersector.o
intersector.cpp: In constructor ‘intersector::intersector(SEXP, SEXP)’:
intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
8 | if (N!=elements.size()) {
| ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
32 | if (current < 0 || current >= nelements) {
| ~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c merge_windows.cpp -o merge_windows.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c pair_reads.cpp -o pair_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c single_reads.cpp -o single_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_profile.o get_rle_counts.o init.o intersector.o merge_windows.o pair_reads.o single_reads.o utils.o /home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-csaw/00new/csaw/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 (csaw)
csaw.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> library(csaw)
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
Loading required package: GenomeInfoDb
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
>
> test_check("csaw")
[E::sam_itr_next] Null iterator
[ FAIL 0 | WARN 35 | SKIP 0 | PASS 2695 ]
[ FAIL 0 | WARN 35 | SKIP 0 | PASS 2695 ]
>
>
> proc.time()
user system elapsed
252.046 5.230 257.758
csaw.Rcheck/csaw-Ex.timings
| name | user | system | elapsed | |
| SEmethods | 1.148 | 0.008 | 1.157 | |
| calculateCPM | 0.265 | 0.000 | 0.265 | |
| checkBimodality | 0.444 | 0.071 | 0.516 | |
| clusterFDR | 0.928 | 0.092 | 1.020 | |
| clusterWindows | 2.030 | 0.016 | 2.047 | |
| clusterWindowsList | 3.523 | 0.040 | 3.563 | |
| combineTests | 0.150 | 0.000 | 0.151 | |
| correlateReads | 0.249 | 0.000 | 0.249 | |
| csawUsersGuide | 0 | 0 | 0 | |
| defunct | 0.001 | 0.000 | 0.000 | |
| detailRanges | 15.469 | 0.732 | 16.206 | |
| empiricalFDR | 0.132 | 0.000 | 0.132 | |
| extractReads | 0.783 | 0.027 | 0.812 | |
| filterWindows | 0.957 | 0.084 | 1.041 | |
| findMaxima | 0.158 | 0.000 | 0.158 | |
| getBestTest | 0.139 | 0.016 | 0.156 | |
| getPESizes | 0.082 | 0.012 | 0.095 | |
| getWidths | 0.571 | 0.012 | 0.584 | |
| maximizeCcf | 0.000 | 0.000 | 0.001 | |
| mergeResults | 0.228 | 0.008 | 0.237 | |
| mergeResultsList | 0.257 | 0.000 | 0.258 | |
| mergeWindows | 0.053 | 0.000 | 0.054 | |
| mergeWindowsList | 0.550 | 0.016 | 0.567 | |
| minimalTests | 0.026 | 0.000 | 0.026 | |
| mixedTests | 0.098 | 0.000 | 0.098 | |
| normFactors | 0.036 | 0.004 | 0.040 | |
| normOffsets | 0.107 | 0.000 | 0.106 | |
| overlapStats | 0.951 | 0.016 | 0.968 | |
| profileSites | 0.814 | 0.012 | 0.826 | |
| readParam | 0.038 | 0.008 | 0.045 | |
| regionCounts | 0.401 | 0.016 | 0.417 | |
| scaledAverage | 0.465 | 0.004 | 0.469 | |
| strandedCounts | 2.189 | 0.016 | 2.205 | |
| upweightSummit | 0.005 | 0.000 | 0.005 | |
| windowCounts | 1.174 | 0.020 | 1.195 | |
| wwhm | 0.103 | 0.000 | 0.103 | |