Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:41:01 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 1437/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oligo 1.66.0 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the oligo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: oligo |
Version: 1.66.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL oligo |
StartedAt: 2023-11-01 20:17:39 -0000 (Wed, 01 Nov 2023) |
EndedAt: 2023-11-01 20:18:25 -0000 (Wed, 01 Nov 2023) |
EllapsedTime: 46.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL oligo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘oligo’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DABG.c -o DABG.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o ParserGzXYS.c: In function ‘gzcountLines’: ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types] 18 | while (!gzeof(file)){ | ^~~~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1594:27: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1594 | ZEXTERN int ZEXPORT gzeof OF((gzFile file)); | ^~ ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 19 | gzgets(file, buffer, 1000); | ^~~~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1491:31: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1491 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); | ^~ ParserGzXYS.c: In function ‘gzxys_header_field’: ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 46 | fp = gzopen(currentFile, "rb"); | ^ ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] 50 | gzgets(fp, buffer, LINEMAX); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1491:31: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1491 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); | ^~ ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 51 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ ParserGzXYS.c: In function ‘R_read_gzxys_files’: ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 134 | fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb"); | ^ ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 138 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from ParserGzXYS.c:4: /usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c baseProfile.c -o baseProfile.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c basecontent.c -o basecontent.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma_common.c -o rma_common.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -llapack -lblas -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** 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 (oligo)