| Back to the "Multiple platform build/check report" | A [B] C D E F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2016-09-21 03:43:52 -0700 (Wed, 21 Sep 2016).
| Package 127/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| biovizBase 1.21.0 Michael Lawrence
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ ERROR ] | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK |
| Package: biovizBase |
| Version: 1.21.0 |
| Command: rm -rf biovizBase.buildbin-libdir biovizBase.Rcheck && mkdir biovizBase.buildbin-libdir biovizBase.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biovizBase.buildbin-libdir biovizBase_1.21.0.tar.gz >biovizBase.Rcheck\00install.out 2>&1 && cp biovizBase.Rcheck\00install.out biovizBase-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biovizBase.buildbin-libdir --install="check:biovizBase-install.out" --force-multiarch --no-vignettes --timings biovizBase_1.21.0.tar.gz |
| StartedAt: 2016-09-20 04:50:22 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 04:56:44 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 382.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biovizBase.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf biovizBase.buildbin-libdir biovizBase.Rcheck && mkdir biovizBase.buildbin-libdir biovizBase.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biovizBase.buildbin-libdir biovizBase_1.21.0.tar.gz >biovizBase.Rcheck\00install.out 2>&1 && cp biovizBase.Rcheck\00install.out biovizBase-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biovizBase.buildbin-libdir --install="check:biovizBase-install.out" --force-multiarch --no-vignettes --timings biovizBase_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/biovizBase.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.21.0'
* 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 whether package 'biovizBase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' calls in package code:
'BSgenome' 'rtracklayer'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genSymbols: no visible binding for global variable 'start_location'
genSymbols: no visible binding for global variable 'end_location'
genSymbols: no visible binding for global variable 'Chromosome'
genSymbols: no visible binding for global variable 'symbol'
transformToLinkInCircle: no visible binding for global variable
'.circle.x'
transformToLinkInCircle: no visible binding for global variable
'.circle.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.y'
mold,ExpressionSet: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
.circle.x .circle.y Chromosome end_location exprs from.x from.y melt
pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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 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-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/i386/biovizBase.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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' ... ERROR
Running examples in 'biovizBase-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crunch
> ### Title: Fetching GRanges from various data source
> ### Aliases: crunch crunch,TxDb-method crunch,EnsDb-method
> ### crunch,GAlignments-method crunch,BamFile-method
>
> ### ** Examples
>
> library(biovizBase)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> data(genesymbol, package = "biovizBase")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> obj <- txdb
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
>
> ## Fetching data from a EnsDb object.
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
call: validityMethod(object)
error: could not find function "dbHasRequiredTables"
Error: package or namespace load failed for 'EnsDb.Hsapiens.v75'
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'biovizBase-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crunch
> ### Title: Fetching GRanges from various data source
> ### Aliases: crunch crunch,TxDb-method crunch,EnsDb-method
> ### crunch,GAlignments-method crunch,BamFile-method
>
> ### ** Examples
>
> library(biovizBase)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> data(genesymbol, package = "biovizBase")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> obj <- txdb
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
>
> ## Fetching data from a EnsDb object.
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
call: validityMethod(object)
error: could not find function "dbHasRequiredTables"
Error: package or namespace load failed for 'EnsDb.Hsapiens.v75'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"D:/biocbld/BBS-3˜1.4-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R: Error while sourcing D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
Test files with failing tests
test_ensdb.R
D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R
Error in BiocGenerics:::testPackage("biovizBase") :
unit tests failed for package biovizBase
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"D:/biocbld/BBS-3˜1.4-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R: Error while sourcing D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
Test files with failing tests
test_ensdb.R
D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R
Error in BiocGenerics:::testPackage("biovizBase") :
unit tests failed for package biovizBase
Execution halted
* 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: 4 ERRORs, 4 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/biovizBase.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("biovizBase")
Loading required package: ensembldb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
call: validityMethod(object)
error: could not find function "dbHasRequiredTables"
Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
RUNIT TEST PROTOCOL -- Tue Sep 20 04:56:25 2016
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R: Error while sourcing D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
Test files with failing tests
test_ensdb.R
D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R
Error in BiocGenerics:::testPackage("biovizBase") :
unit tests failed for package biovizBase
Execution halted
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> BiocGenerics:::testPackage("biovizBase")
Loading required package: ensembldb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
call: validityMethod(object)
error: could not find function "dbHasRequiredTables"
Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
RUNIT TEST PROTOCOL -- Tue Sep 20 04:56:36 2016
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R: Error while sourcing D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R : Error : package or namespace load failed for 'EnsDb.Hsapiens.v75'
Test files with failing tests
test_ensdb.R
D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/unitTests/test_ensdb.R
Error in BiocGenerics:::testPackage("biovizBase") :
unit tests failed for package biovizBase
Execution halted
biovizBase.Rcheck/00install.out:
install for i386
* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/R_ext/RS.h:31:0,
from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:33,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/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 'biovizBase' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/R_ext/RS.h:31:0,
from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:33,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.21.0.zip
* DONE (biovizBase)
biovizBase.Rcheck/examples_i386/biovizBase-Ex.timings:
| name | user | system | elapsed | |
| CRC | 0 | 0 | 0 | |
| GCcontent | 0.69 | 0.03 | 1.26 | |
| addStepping-method | 0.53 | 0.00 | 0.53 | |
| aes-utils | 0 | 0 | 0 | |
| colorBlindSafePal | 0 | 0 | 0 | |
| containLetters | 0 | 0 | 0 | |
| crc1.GeRL | 0.01 | 0.00 | 0.02 | |
biovizBase.Rcheck/examples_x64/biovizBase-Ex.timings:
| name | user | system | elapsed | |
| CRC | 0.00 | 0.02 | 0.01 | |
| GCcontent | 0.92 | 0.00 | 0.92 | |
| addStepping-method | 0.61 | 0.00 | 0.61 | |
| aes-utils | 0 | 0 | 0 | |
| colorBlindSafePal | 0 | 0 | 0 | |
| containLetters | 0 | 0 | 0 | |
| crc1.GeRL | 0.01 | 0.00 | 0.02 | |