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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the hapFabia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hapFabia.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 838/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hapFabia 1.34.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: hapFabia |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hapFabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hapFabia_1.34.0.tar.gz |
| StartedAt: 2021-10-15 00:16:02 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:18:00 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 117.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hapFabia.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hapFabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hapFabia_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hapFabia/DESCRIPTION' ... OK
* this is package 'hapFabia' version '1.34.0'
* 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 whether package 'hapFabia' can be installed ... WARNING
Found the following significant warnings:
vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck/00install.out' for details.
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
File 'hapFabia/R/zzz.R':
.onLoad calls:
packageStartupMessage("+--------------------------+ # # ## ##### \n", "|#.....#...#.......#.#....#| # # # # # # \n", "|#.....#...#.......#.#....#| ###### # # # # \n", "|#.....#...#...............| # # ###### ##### \n", "|#.....#...#.......#.#....#| # # # # # \n", "|#.....#...#...............| # # # # # \n", "|#.....#...#.......#.#....#| ####### \n", "|..................#.#....#| # ## ##### # ## \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "|..................#.#....#| ##### # # ##### # # # \n", "|#.....#...#.......#.#....#| # ###### # # # ###### \n", "|#.....#...#.......#.#....#| # # # # # # # # \n", "+--------------------------+ # # # ##### # # # \n")
packageStartupMessage("Citation: S. Hochreiter,", "\n", "HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,", "\n", "Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.", "\n", "BibTex: enter 'toBibtex(citation(\"hapFabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html", "\n\n", "hapFabia Package Version ", version, "\n")
See section 'Good practice' in '?.onAttach'.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... OK
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/hapFabia/libs/i386/hapFabia.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/hapFabia/libs/x64/hapFabia.dll':
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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
iterateIntervals 5.53 0.74 6.27
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/hapFabia.Rcheck/00check.log'
for details.
hapFabia.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/hapFabia_1.34.0.tar.gz && rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL hapFabia_1.34.0.zip && rm hapFabia_1.34.0.tar.gz hapFabia_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
98 955k 98 941k 0 0 1587k 0 --:--:-- --:--:-- --:--:-- 1587k
100 955k 100 955k 0 0 1609k 0 --:--:-- --:--:-- --:--:-- 1608k
install for i386
* installing *source* package 'hapFabia' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ch == EOF)
^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
while (idx > *linebufsz - 2) {
^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(format[j],Iformat,19);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
strncat(info[j],Iinfo,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(filter[j],Ifilter,19);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(qual[j],Iqual,19);
^~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
strncat(minor[j],Iminor,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
strncat(major[j],Imajor,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
strncat(snpName[j],IsnpName,49);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/hapFabia.buildbin-libdir/00LOCK-hapFabia/00new/hapFabia/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'hapFabia'
finding HTML links ... done
IBDsegment-class html
REDIRECT:topic IBDsegment,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method -> IBDsegment-class.html [ FAIL ]
IBDsegmentList-class html
IBDsegmentList2excel html
analyzeIBDsegments html
chr1ASW1000G html
compareIBDsegmentLists html
extractIBDsegments html
REDIRECT:topic extractIBDsegments,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method -> extractIBDsegments.html [ FAIL ]
findDenseRegions html
hapFabia html
hapFabiaVersion html
hapRes html
identifyDuplicates html
iterateIntervals html
makePipelineFile html
matrixPlot html
mergeIBDsegmentLists html
mergedIBDsegmentList html
plotIBDsegment html
res html
setAnnotation html
setStatistics html
sim html
simu html
simulateIBDsegments html
simulateIBDsegmentsFabia html
split_sparse_matrix html
toolsFactorizationClass html
vcftoFABIA html
** 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
install for x64
* installing *source* package 'hapFabia' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (ch == EOF)
^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
while (idx > *linebufsz - 2) {
^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(format[j],Iformat,19);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
strncat(info[j],Iinfo,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(filter[j],Ifilter,19);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
strncat(qual[j],Iqual,19);
^~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
strncat(minor[j],Iminor,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
strncat(major[j],Imajor,190);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
strncat(snpName[j],IsnpName,49);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.34.0.zip
* DONE (hapFabia)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'hapFabia' successfully unpacked and MD5 sums checked
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hapFabia.Rcheck/examples_i386/hapFabia-Ex.timings
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hapFabia.Rcheck/examples_x64/hapFabia-Ex.timings
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