Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 276/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
casper 2.40.0 (landing page) David Rossell
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the casper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/casper.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: casper |
Version: 2.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings casper_2.40.0.tar.gz |
StartedAt: 2024-11-19 23:53:35 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:57:55 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 260.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: casper.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings casper_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘casper/DESCRIPTION’ ... OK * this is package ‘casper’ version ‘2.40.0’ * 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 ‘casper’ can be installed ... WARNING Found the following significant warnings: cstat.cpp:1111:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] cstat.cpp:1117:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 8)))’ and NULL [-Waddress] cstat.cpp:1123:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] cstat.cpp:1131:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))’ and NULL [-Waddress] cstat.cpp:1133:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] cstat.cpp:1141:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))’ and NULL [-Waddress] cstat.cpp:1143:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘<unknown>’ [-Wrestrict] seppel.cpp:484:19: warning: ‘void operator delete [](void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict] See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: data 1.2Mb libs 3.7Mb * 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 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 ... NOTE checkRd: (-1) asymmetryCheck.Rd:21: Lost braces 21 | \item{...}{Other arguments to be passed on to code{plot}} | ^ checkRd: (-1) qqnormGenomeWide.Rd:35: Lost braces 35 | \item{...}{Other arguments to be passed on to code{plot}} | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00check.log’ for details.
casper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL casper ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘casper’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c casper.cpp -o casper.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cstat.cpp -o cstat.o cstat.cpp: In function ‘void free_vector(float*, int, int)’: cstat.cpp:1111:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] 1111 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_dvector(double*, int, int)’: cstat.cpp:1117:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 8)))’ and NULL [-Waddress] 1117 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_ivector(int*, int, int)’: cstat.cpp:1123:20: warning: comparing the result of pointer addition ‘(v + ((sizetype)(((long unsigned int)nl) * 4)))’ and NULL [-Waddress] 1123 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function ‘void free_dmatrix(double**, int, int, int, int)’: cstat.cpp:1131:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))’ and NULL [-Waddress] 1131 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1133:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] 1133 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ cstat.cpp: In function ‘void free_imatrix(int**, int, int, int, int)’: cstat.cpp:1141:47: warning: comparing the result of pointer addition ‘((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))’ and NULL [-Waddress] 1141 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1143:21: warning: comparing the result of pointer addition ‘(m + ((sizetype)(((long unsigned int)nrl) * 8)))’ and NULL [-Waddress] 1143 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dataframe.cpp -o dataframe.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c discretedf.cpp -o discretedf.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dropVariant.cpp -o dropVariant.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exon.cpp -o exon.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fragFunc.c -o fragFunc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fragment.cpp -o fragment.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c functions.c -o functions.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c join_exons.c -o join_exons.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c makeIslands.c -o makeIslands.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c model.cpp -o model.o In file included from /usr/include/stdio.h:980, from model.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* Model::toString()’ at model.cpp:147:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘<unknown>’ [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c model_cmp.cpp -o model_cmp.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pathCounts.c -o pathCounts.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c procBam.c -o procBam.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rcasper.cpp -o rcasper.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c seppel.cpp -o seppel.o seppel.cpp: In member function ‘void Seppel::exploreUnif(int, std::set<Variant*, VariantCmp>*)’: seppel.cpp:484:9: warning: array subscript -1 is outside array bounds of ‘void [24]’ [-Warray-bounds=] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~~~~~~~~~~~ seppel.cpp:402:55: note: at offset -8 into object of size 24 allocated by ‘operator new’ 402 | vector<Model*>* possiblemodels = new vector<Model*>(); | ^ seppel.cpp:484:19: warning: ‘void operator delete [](void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~ seppel.cpp:402:55: note: returned from ‘void* operator new(std::size_t)’ 402 | vector<Model*>* possiblemodels = new vector<Model*>(); | ^ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simReads.c -o simReads.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c smartmodeldist.cpp -o smartmodeldist.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uniqQname.c -o uniqQname.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c variant.cpp -o variant.o In file included from /usr/include/stdio.h:980, from variant.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void Variant::toString(char*)’ at variant.cpp:164:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ variant.cpp: In member function ‘void Variant::toString(char*)’: variant.cpp:156:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 156 | void Variant::toString(char *str) | ~~~~~~^~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c variant_cmp.cpp -o variant_cmp.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-casper/00new/casper/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘transcripts’ in package ‘casper’ ** 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 (casper)
casper.Rcheck/casper-Ex.timings
name | user | system | elapsed | |
K562.r1l1 | 0.089 | 0.010 | 0.100 | |
annotatedGenome-class | 0.000 | 0.001 | 0.001 | |
asymmetryCheck | 0.008 | 0.001 | 0.009 | |
calcDenovo | 0 | 0 | 0 | |
calcExp | 2.948 | 0.140 | 3.088 | |
denovoExpr | 2.646 | 0.274 | 2.921 | |
denovoGeneExpr-class | 0.000 | 0.000 | 0.001 | |
denovoGenomeExpr-class | 0.001 | 0.000 | 0.000 | |
distrsGSE37704 | 0.097 | 0.005 | 0.102 | |
genePlot | 0.208 | 0.005 | 0.214 | |
getDistrs | 0.257 | 0.005 | 0.263 | |
getIsland | 0.084 | 0.004 | 0.088 | |
getNreads | 0 | 0 | 0 | |
getReads | 0 | 0 | 0 | |
getRoc | 0 | 0 | 0 | |
hg19DB | 0.077 | 0.003 | 0.080 | |
mergeBatches | 0.056 | 0.000 | 0.055 | |
mergeExp | 0 | 0 | 0 | |
modelPrior | 0.259 | 0.005 | 0.265 | |
modelPriorAS-class | 0 | 0 | 0 | |
pathCounts-class | 0 | 0 | 0 | |
pathCounts | 0 | 0 | 0 | |
plot-methods | 0 | 0 | 0 | |
plotExpr | 0.001 | 0.000 | 0.000 | |
plotPriorAS | 0 | 0 | 0 | |
probNonEquiv | 0.058 | 0.001 | 0.059 | |
procBam-class | 0.001 | 0.000 | 0.001 | |
procBam | 0 | 0 | 0 | |
procGenome | 0.001 | 0.000 | 0.000 | |
qqnormGenomeWide | 0.034 | 0.001 | 0.035 | |
quantileNorm | 0.008 | 0.000 | 0.009 | |
relexprByGene | 0 | 0 | 0 | |
rmShortInserts | 0 | 0 | 0 | |
simMAE | 0 | 0 | 0 | |
simMAEcheck | 0 | 0 | 0 | |
simMultSamples | 0 | 0 | 0 | |
simReads | 0.262 | 0.010 | 0.271 | |
simulatedSamples-class | 0.001 | 0.000 | 0.000 | |
splitGenomeByLength | 0 | 0 | 0 | |
transcripts | 0.138 | 0.003 | 0.141 | |
wrapDenovo | 0.000 | 0.001 | 0.000 | |
wrapKnown | 0 | 0 | 0 | |