BioC 3.2: CHECK report for CNEr on moscato1
This page was generated on 2016-04-23 10:20:00 -0700 (Sat, 23 Apr 2016).
CNEr 1.6.2
Ge Tan
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CNEr | | Last Changed Rev: 111508 / Revision: 116712 | | Last Changed Date: 2015-12-15 08:48:05 -0800 (Tue, 15 Dec 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
Summary
| Package: CNEr
|
| Version: 1.6.2
|
| Command: rm -rf CNEr.buildbin-libdir CNEr.Rcheck && mkdir CNEr.buildbin-libdir CNEr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNEr.buildbin-libdir CNEr_1.6.2.tar.gz >CNEr.Rcheck\00install.out 2>&1 && cp CNEr.Rcheck\00install.out CNEr-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CNEr.buildbin-libdir --install="check:CNEr-install.out" --force-multiarch --no-vignettes --timings CNEr_1.6.2.tar.gz
|
| StartedAt: 2016-04-23 00:50:17 -0700 (Sat, 23 Apr 2016)
|
| EndedAt: 2016-04-23 00:56:33 -0700 (Sat, 23 Apr 2016)
|
| EllapsedTime: 376.2 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: CNEr.Rcheck
|
| Warnings: 1
|
Command output
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###
### Running command:
###
### rm -rf CNEr.buildbin-libdir CNEr.Rcheck && mkdir CNEr.buildbin-libdir CNEr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNEr.buildbin-libdir CNEr_1.6.2.tar.gz >CNEr.Rcheck\00install.out 2>&1 && cp CNEr.Rcheck\00install.out CNEr-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CNEr.buildbin-libdir --install="check:CNEr-install.out" --force-multiarch --no-vignettes --timings CNEr_1.6.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CNEr.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNEr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNEr' version '1.6.2'
* 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 'CNEr' can be installed ... WARNING
Found the following significant warnings:
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
See 'D:/biocbld/bbs-3.2-bioc/meat/CNEr.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 ... 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 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/i386/CNEr.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.2-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64/CNEr.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [12s] OK
** running examples for arch 'x64' ... [14s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [9s]
[9s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [9s]
[10s] 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, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/CNEr.Rcheck/00check.log'
for details.
CNEr.Rcheck/00install.out:
install for i386
* installing *source* package 'CNEr' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
ceScan.c: In function 'myCeScan':
ceScan.c:865:28: warning: unused variable 'i' [-Wunused-variable]
ceScan.c:865:7: warning: unused variable 'nrCNE' [-Wunused-variable]
ceScan.c:862:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c: In function 'myCeScanFile':
ceScan.c:895:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:472:8: warning: 'e' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m32 -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'CNEr' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
ceScan.c: In function 'myCeScan':
ceScan.c:865:28: warning: unused variable 'i' [-Wunused-variable]
ceScan.c:865:7: warning: unused variable 'nrCNE' [-Wunused-variable]
ceScan.c:862:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c: In function 'myCeScanFile':
ceScan.c:895:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m64 -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.6.2.zip
* DONE (CNEr)
CNEr.Rcheck/examples_i386/CNEr-Ex.timings:
| name | user | system | elapsed
|
| Axt-util | 0.10 | 0.00 | 0.09 |
|
| CNE-class | 0 | 0 | 0 |
|
| CNEDensity | 0.86 | 0.02 | 0.89 |
|
| CNEHg19DanRer7 | 0.03 | 0.00 | 0.03 |
|
| axisTrack | 0.00 | 0.02 | 0.02 |
|
| axt-class | 0 | 0 | 0 |
|
| axtDanRer7Hg19 | 0.00 | 0.01 | 0.01 |
|
| axtInfo | 0 | 0 | 0 |
|
| binner | 0 | 0 | 0 |
|
| blatCNE | 0.01 | 0.00 | 0.02 |
|
| ceScan-methods | 0 | 0 | 0 |
|
| cneBlatedDanRer7Hg19 | 0.02 | 0.00 | 0.02 |
|
| cneHg19DanRer7_45_50 | 0.01 | 0.00 | 0.01 |
|
| cneMerge | 0.60 | 0.03 | 0.63 |
|
| fetchChromSizes | 0.06 | 0.00 | 1.13 |
|
| finalCNE | 0 | 0 | 0 |
|
| qSizesDanRer7 | 0.00 | 0.02 | 0.02 |
|
| readAxt | 0 | 0 | 0 |
|
| readBed | 0.03 | 0.00 | 0.03 |
|
| readCNERangesFromSQLite | 0.01 | 0.00 | 0.01 |
|
| reverseCigar | 0 | 0 | 0 |
|
| saveCNEToSQLite | 0.16 | 0.00 | 0.69 |
|
| subAxt-methods | 0 | 0 | 0 |
|
| writeAxt | 0 | 0 | 0 |
|
CNEr.Rcheck/examples_x64/CNEr-Ex.timings:
| name | user | system | elapsed
|
| Axt-util | 0.10 | 0.00 | 0.11 |
|
| CNE-class | 0 | 0 | 0 |
|
| CNEDensity | 1.06 | 0.02 | 1.07 |
|
| CNEHg19DanRer7 | 0.03 | 0.00 | 0.04 |
|
| axisTrack | 0.00 | 0.01 | 0.02 |
|
| axt-class | 0 | 0 | 0 |
|
| axtDanRer7Hg19 | 0.01 | 0.00 | 0.01 |
|
| axtInfo | 0 | 0 | 0 |
|
| binner | 0.02 | 0.00 | 0.02 |
|
| blatCNE | 0 | 0 | 0 |
|
| ceScan-methods | 0 | 0 | 0 |
|
| cneBlatedDanRer7Hg19 | 0.03 | 0.00 | 0.03 |
|
| cneHg19DanRer7_45_50 | 0.01 | 0.00 | 0.02 |
|
| cneMerge | 1.02 | 0.02 | 1.03 |
|
| fetchChromSizes | 0.05 | 0.02 | 1.10 |
|
| finalCNE | 0 | 0 | 0 |
|
| qSizesDanRer7 | 0 | 0 | 0 |
|
| readAxt | 0 | 0 | 0 |
|
| readBed | 0.02 | 0.00 | 0.01 |
|
| readCNERangesFromSQLite | 0.01 | 0.00 | 0.02 |
|
| reverseCigar | 0 | 0 | 0 |
|
| saveCNEToSQLite | 0.11 | 0.00 | 0.12 |
|
| subAxt-methods | 0 | 0 | 0 |
|
| writeAxt | 0 | 0 | 0 |
|