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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rtracklayer
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:268:11: warning: ‘ans_nhits’ may be used uninitialized [-Wmaybe-uninitialized]
268 | INTEGER(ans_nhits)[i] = nqhits;
| ^~~~~~~~~~~~~~~~~~
bigWig.c:231:58: note: ‘ans_nhits’ was declared here
231 | SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o
In file included from /usr/include/string.h:548,
from ucsc/common.h:33,
from bigBedHelper.h:5,
from bigBedHelper.c:1:
In function ‘strncpy’,
inlined from ‘bbNamedFileChunkKey’ at bigBedHelper.c:148:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBed.c -o bigBed.o
bigBed.c: In function ‘BBDFile_write’:
bigBed.c:338:10: warning: variable ‘extraIndexListEndOffset’ set but not used [-Wunused-but-set-variable]
338 | bits64 extraIndexListEndOffset = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function ‘BBDFile_query’:
bigBed.c:195:7: warning: ‘name’ may be used uninitialized [-Wmaybe-uninitialized]
195 | SET_STRING_ELT(name, i, mkChar(bed->name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:74:54: note: ‘name’ was declared here
74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
| ^~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized]
198 | INTEGER(score)[i] = bed->score;
| ^~~~~~~~~~~~~~
bigBed.c:74:60: note: ‘score’ was declared here
74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
| ^~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized [-Wmaybe-uninitialized]
205 | INTEGER(thickStart)[i] = bed->thickStart;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:26: note: ‘thickStart’ was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized [-Wmaybe-uninitialized]
204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:38: note: ‘thickWidth’ was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~~~~
bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized [-Wmaybe-uninitialized]
209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:50: note: ‘itemRgb’ was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized [-Wmaybe-uninitialized]
218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:59: note: ‘blocks’ was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized [-Wmaybe-uninitialized]
236 | INTEGER(lengthIndex)[efIndex] = index + 1;
| ^~~~~~~~~~~~~~~~~~~~
bigBed.c:76:31: note: ‘lengthIndex’ was declared here
76 | extraFields = R_NilValue, lengthIndex;
| ^~~~~~~~~~~
bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized [-Wmaybe-uninitialized]
226 | switch(typeId[efIndex]) {
| ^
bigBed.c:141:13: note: ‘typeId’ was declared here
141 | SEXPTYPE *typeId;
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o
ucsc/binRange.c:49:12: warning: ‘binFromRangeExtended’ defined but not used [-Wunused-function]
49 | static int binFromRangeExtended(int start, int end)
| ^~~~~~~~~~~~~~~~~~~~
ucsc/binRange.c:28:12: warning: ‘binFromRangeStandard’ defined but not used [-Wunused-function]
28 | static int binFromRangeStandard(int start, int end)
| ^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/asParse.c -o ucsc/asParse.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function ‘bedParseRgb’:
ucsc/basicBed.c:449:1: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
449 | strncpy(dupe, itemRgb, sizeof(dupe));
| ^
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c:326:31: warning: ‘bigBedIntervalsMatchingName’ defined but not used [-Wunused-function]
326 | static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/bigBed.c:311:16: warning: ‘bbWordIsInHash’ defined but not used [-Wunused-function]
311 | static boolean bbWordIsInHash(char *line, int fieldIx, void *target)
| ^~~~~~~~~~~~~~
ucsc/bigBed.c:301:16: warning: ‘bbWordMatchesName’ defined but not used [-Wunused-function]
301 | static boolean bbWordMatchesName(char *line, int fieldIx, void *target)
| ^~~~~~~~~~~~~~~~~
ucsc/bigBed.c:252:31: warning: ‘bigBedChunksMatchingNames’ defined but not used [-Wunused-function]
252 | static struct fileOffsetSize *bigBedChunksMatchingNames(struct bbiFile *bbi,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/bigBed.c:241:31: warning: ‘bigBedChunksMatchingName’ defined but not used [-Wunused-function]
241 | static struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi,
| ^~~~~~~~~~~~~~~~~~~~~~~~
ucsc/bigBed.c:150:28: warning: ‘bigBedCoverageIntervals’ defined but not used [-Wunused-function]
150 | static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi,
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’:
ucsc/bwgQuery.c:164:25: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
164 | char *blockPt, *blockEnd;
| ^~~~~~~~
ucsc/bwgQuery.c: At top level:
ucsc/bwgQuery.c:47:12: warning: ‘bigWigBlockDumpIntersectingRange’ defined but not used [-Wunused-function]
47 | static int bigWigBlockDumpIntersectingRange(boolean isSwapped, char *blockPt, char *blockEnd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:530:13: warning: ‘rEnumerateBlocks’ defined but not used [-Wunused-function]
530 | static void rEnumerateBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset,
| ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1971:13: warning: ‘dateAdd’ defined but not used [-Wunused-function]
1971 | static void dateAdd(struct tm *tp,int addYears,int addMonths,int addDays)
| ^~~~~~~
ucsc/common.c:1901:14: warning: ‘emptyStr’ defined but not used [-Wunused-variable]
1901 | static char *emptyStr = "";
| ^~~~~~~~
ucsc/common.c:1900:14: warning: ‘naStr’ defined but not used [-Wunused-variable]
1900 | static char *naStr = "n/a";
| ^~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:521:12: warning: ‘findHeadPolyTMaybeMask’ defined but not used [-Wunused-function]
521 | static int findHeadPolyTMaybeMask(DNA *dna, int size, boolean doMask,
| ^~~~~~~~~~~~~~~~~~~~~~
ucsc/dnautil.c:465:12: warning: ‘findTailPolyAMaybeMask’ defined but not used [-Wunused-function]
465 | static int findTailPolyAMaybeMask(DNA *dna, int size, boolean doMask,
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:255:5: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
255 | write(STDERR_FILENO, errMsg, strlen(errMsg));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/errAbort.c: At top level:
ucsc/errAbort.c:218:13: warning: ‘warnAbortHandler’ defined but not used [-Wunused-function]
218 | static void warnAbortHandler(char *format, va_list args)
| ^~~~~~~~~~~~~~~~
ucsc/errAbort.c:210:13: warning: ‘debugAbort’ defined but not used [-Wunused-function]
210 | static void debugAbort()
| ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c:14:12: warning: ‘_dotForUserMod’ defined but not used [-Wunused-variable]
14 | static int _dotForUserMod = 100; /* How often does dotForUser() output a dot. */
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
ucsc/rangeTree.c:36:14: warning: ‘sumInt’ defined but not used [-Wunused-function]
36 | static void *sumInt(void *a, void *b)
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
ucsc/rbTree.c:680:13: warning: ‘addRefWithContext’ defined but not used [-Wunused-function]
680 | static void addRefWithContext(void *item, void *context)
| ^~~~~~~~~~~~~~~~~
ucsc/rbTree.c:674:13: warning: ‘addRef’ defined but not used [-Wunused-function]
674 | static void addRef(void *item)
| ^~~~~~
ucsc/rbTree.c:576:13: warning: ‘rTreeDump’ defined but not used [-Wunused-function]
576 | static void rTreeDump(struct rbTreeNode *n)
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c:357:14: warning: ‘memTrackerRealloc’ defined but not used [-Wunused-function]
357 | static void *memTrackerRealloc(void *vpt, size_t size)
| ^~~~~~~~~~~~~~~~~
ucsc/memalloc.c:348:13: warning: ‘memTrackerFree’ defined but not used [-Wunused-function]
348 | static void memTrackerFree(void *vpt)
| ^~~~~~~~~~~~~~
ucsc/memalloc.c:314:26: warning: ‘carefulMemHandler’ defined but not used [-Wunused-variable]
314 | static struct memHandler carefulMemHandler =
| ^~~~~~~~~~~~~~~~~
ucsc/memalloc.c:220:13: warning: ‘carefulMemInit’ defined but not used [-Wunused-function]
220 | static void carefulMemInit(size_t maxToAlloc)
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
ucsc/dlist.c:124:12: warning: ‘dlNodeCmp’ defined but not used [-Wunused-function]
124 | static int dlNodeCmp(const void *elem1, const void *elem2)
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/filePath.c -o ucsc/filePath.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘djb2_hash’:
ucsc/udc.c:1070:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
1070 | while (c = *str++)
| ^
ucsc/udc.c: At top level:
ucsc/udc.c:1273:13: warning: ‘qDecode’ defined but not used [-Wunused-function]
1273 | static void qDecode(const char *input, char *buf, size_t size)
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
ucsc/net.c: In function ‘netUrlOpenSockets’:
ucsc/net.c:168:22: warning: unused variable ‘status’ [-Wunused-variable]
168 | CURLcode status = wrapped_curl_request(curl, GET);
| ^~~~~~
ucsc/net.c: In function ‘header_get_last_modified’:
ucsc/net.c:36:1: warning: control reaches end of non-void function [-Wreturn-type]
36 | }
| ^
ucsc/net.c: In function ‘header_get_content_length’:
ucsc/net.c:57:1: warning: control reaches end of non-void function [-Wreturn-type]
57 | }
| ^
ucsc/net.c: In function ‘netUrlOpenSockets’:
ucsc/net.c:187:1: warning: control reaches end of non-void function [-Wreturn-type]
187 | }
| ^
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
ucsc/https.c: In function ‘openSslInit’:
ucsc/https.c:76:5: warning: ‘ERR_load_SSL_strings’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
76 | ERR_load_SSL_strings();
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/openssl/sslerr.h:17,
from /usr/include/openssl/ssl.h:43,
from ucsc/https.c:8:
/usr/include/openssl/sslerr_legacy.h:29:27: note: declared here
29 | OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void);
| ^~~~~~~~~~~~~~~~~~~~
ucsc/https.c: At top level:
ucsc/https.c:27:13: warning: ‘openssl_locking_callback’ defined but not used [-Wunused-function]
27 | static void openssl_locking_callback(int mode, int n, const char * file, int line)
| ^~~~~~~~~~~~~~~~~~~~~~~~
ucsc/https.c:22:22: warning: ‘openssl_id_callback’ defined but not used [-Wunused-function]
22 | static unsigned long openssl_id_callback(void)
| ^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/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/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/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 -lcurl -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)
