biovizBase 1.24.0
Michael Lawrence
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/biovizBase | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/biovizBase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.24.0’
* 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 ‘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
* 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 ... OK
* 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
crunch-method 17.656 0.248 20.372
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/biovizBase.Rcheck/00check.log’
for details.
* installing *source* package ‘biovizBase’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bin_offsets.c -o bin_offsets.o
In file included from /usr/include/string.h:630:0,
from /home/biocbuild/bbs-3.5-bioc/R/include/R_ext/RS.h:34,
from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/R_ext/RS.h:34:0,
from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
/usr/include/string.h:394:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
extern size_t strlen (const char *__s)
^
In file included from /usr/include/string.h:630:0,
from /home/biocbuild/bbs-3.5-bioc/R/include/R_ext/RS.h:34,
from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
bin_offsets.c:57:15: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
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 /home/biocbuild/bbs-3.5-bioc/R/include/R_ext/RS.h:34:0,
from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
/usr/include/string.h:143:12: note: expected ‘const char *’ but argument is of type ‘Rbyte * {aka unsigned char *}’
extern int strncmp (const char *__s1, const char *__s2, size_t __n)
^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/biovizBase.Rcheck/biovizBase/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 (biovizBase)