| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:15 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 | ||||
|
To the developers/maintainers of the rtracklayer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1758/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.61.0 (landing page) Michael Lawrence
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: rtracklayer |
| Version: 1.61.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings rtracklayer_1.61.0.tar.gz |
| StartedAt: 2023-05-26 04:55:25 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:55:39 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 14.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rtracklayer.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:rtracklayer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings rtracklayer_1.61.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘rtracklayer/DESCRIPTION’ ... OK
* this is package ‘rtracklayer’ version ‘1.61.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
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 ‘rtracklayer’ can be installed ... WARNING
Found the following significant warnings:
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.8Mb
libs 2.2Mb
* 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 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 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘rtracklayer.Rnw’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘rtracklayer.Rnw’
...
> proc.time()
user system elapsed
0.187 0.019 0.201
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/rtracklayer.Rcheck/00check.log’
for details.
rtracklayer.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c bigWig.c -o bigWig.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c bigBedHelper.c -o bigBedHelper.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c bigBed.c -o bigBed.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c chain_io.c -o chain_io.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/aliType.c -o ucsc/aliType.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/asParse.c -o ucsc/asParse.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/basicBed.c -o ucsc/basicBed.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bigBed.c -o ucsc/bigBed.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
In function ‘writeIndexLevel’,
inlined from ‘bptFileBulkIndexToOpenFile’ at ucsc/bPlusTree.c:567:29:
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
461 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function ‘bptFileBulkIndexToOpenFile’:
ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
460 | char keyBuf[keySize+1];
| ^~~~~~
In function ‘writeLeafLevel’,
inlined from ‘bptFileBulkIndexToOpenFile’ at ucsc/bPlusTree.c:575:1:
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
513 | keyBuf[keySize] = 0;
| ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function ‘bptFileBulkIndexToOpenFile’:
ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
512 | char keyBuf[keySize+1];
| ^~~~~~
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/hex.c -o ucsc/hex.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/filePath.c -o ucsc/filePath.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/udc.c -o ucsc/udc.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/net.c -o ucsc/net.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/internet.c -o ucsc/internet.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
** 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 (rtracklayer)