Ge Tan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CNEr |
| Branch: RELEASE_3_6 |
| Last Commit: b8634d6 |
| Last Changed Date: 2017-10-30 12:40:11 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:11:52 -0400 (Thu, 12 Apr 2018).
| Package 258/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNEr 1.14.0 Ge Tan
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: CNEr |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.14.0.tar.gz |
| StartedAt: 2018-04-11 22:22:22 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:31:49 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 566.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CNEr.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CNEr_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CNEr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNEr’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.7Mb
sub-directories of 1Mb or more:
doc 1.9Mb
extdata 15.9Mb
libs 1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘CNEr/libs/CNEr.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Object: ‘ucsc/errabort.o’
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘ucsc/pipeline.o’
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘ucsc/obscure.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
‘ucsc/verbose.o’, ‘ucsc/os.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’,
‘ucsc/os.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeGRBs 278.884 5.200 285.956
plotCNEWidth 7.340 0.096 7.442
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/CNEr.Rcheck/00check.log’
for details.
CNEr.Rcheck/00install.out
* installing *source* package ‘CNEr’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -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]
int _binNextShift = binNextShift();
^
utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c io.c -o io.o
io.c: In function ‘myReadAxt’:
io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable]
struct axt *axt=NULL, *curAxt;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ceScan.c -o ceScan.o
ceScan.c: In function ‘ceScan’:
ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable]
char rest, path[PATH_LEN];
^
ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable]
int i, n;
^
ceScan.c: In function ‘freeSlThreshold’:
ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c: In function ‘myCeScan’:
ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c: In function ‘myCeScanFile’:
ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘byteSwap64’:
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -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]
int pastPoly = 0;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -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]
long long discardMe = 0;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o CNEr.so 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 -lz -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/CNEr.Rcheck/CNEr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNEr)
CNEr.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CNEr)
>
> test_check("CNEr")
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
══ testthat results ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
19.044 0.192 19.959
CNEr.Rcheck/CNEr-Ex.timings
| name | user | system | elapsed | |
| AssemblyStats | 0.016 | 0.004 | 0.245 | |
| Axt-class | 2.084 | 0.020 | 2.105 | |
| Axt-util | 0.032 | 0.000 | 0.031 | |
| CNE-class | 0.268 | 0.004 | 0.270 | |
| CNEDanRer10Hg38 | 0.020 | 0.000 | 0.019 | |
| CNEDensity | 1.000 | 0.012 | 1.010 | |
| GRangePairs-class | 0.452 | 0.004 | 0.458 | |
| addAncestorGO | 0 | 0 | 0 | |
| axisTrack | 0.004 | 0.000 | 0.004 | |
| axtChain | 0.000 | 0.000 | 0.001 | |
| axtInfo | 0.000 | 0.000 | 0.001 | |
| binner | 0.004 | 0.000 | 0.003 | |
| blatCNE | 0.000 | 0.000 | 0.001 | |
| ceScan-methods | 1.088 | 0.028 | 2.106 | |
| chainMergeSort | 0.000 | 0.000 | 0.001 | |
| chainNetSyntenic | 0.000 | 0.000 | 0.001 | |
| chainPreNet | 0.004 | 0.000 | 0.001 | |
| cneFinalListDanRer10Hg38 | 0.052 | 0.000 | 0.053 | |
| cneMerge | 0.712 | 0.008 | 0.726 | |
| fetchChromSizes | 0 | 0 | 0 | |
| fixCoordinates | 0.460 | 0.012 | 0.471 | |
| grangesPairsForDotplot | 0.004 | 0.000 | 0.003 | |
| last | 0 | 0 | 0 | |
| lastz | 0.000 | 0.000 | 0.001 | |
| lavToPsl | 0 | 0 | 0 | |
| makeAncoraFiles | 0.040 | 0.000 | 0.039 | |
| makeAxtTracks | 0.256 | 0.004 | 0.259 | |
| makeCNEDensity | 0 | 0 | 0 | |
| makeGRBs | 278.884 | 5.200 | 285.956 | |
| matchDistribution | 0.78 | 0.00 | 0.78 | |
| netToAxt | 0.000 | 0.000 | 0.001 | |
| orgKEGGIds2EntrezIDs | 0.000 | 0.000 | 0.001 | |
| plotCNEDistribution | 1.260 | 0.016 | 1.275 | |
| plotCNEWidth | 7.340 | 0.096 | 7.442 | |
| psubAxt | 0.372 | 0.000 | 0.371 | |
| read.rmMask.GRanges | 0.024 | 0.000 | 0.033 | |
| read.rmskFasta | 0.048 | 0.000 | 0.052 | |
| readAncora | 0.084 | 0.000 | 0.090 | |
| readAncoraIntoSQLite | 0.988 | 0.004 | 0.994 | |
| readAxt | 0.028 | 0.000 | 0.028 | |
| readBed | 0.012 | 0.000 | 0.013 | |
| readCNERangesFromSQLite | 0.06 | 0.00 | 0.06 | |
| reverseCigar | 0.004 | 0.000 | 0.001 | |
| saveCNEToSQLite | 0.160 | 0.000 | 0.162 | |
| scoringMatrix | 0.004 | 0.000 | 0.000 | |
| subAxt-methods | 0.764 | 0.008 | 0.772 | |
| syntenicDotplot | 1.644 | 0.204 | 3.811 | |
| writeAxt | 0.024 | 0.000 | 0.024 | |