Michael Lawrence
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/biovizBase |
| Branch: RELEASE_3_8 |
| Last Commit: b6776d0 |
| Last Changed Date: 2018-12-11 14:49:53 -0400 (Tue, 11 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:23 -0400 (Tue, 16 Apr 2019).
| Package 162/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biovizBase 1.30.1 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: biovizBase |
| Version: 1.30.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings biovizBase_1.30.1.tar.gz |
| StartedAt: 2019-04-15 22:32:23 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:37:02 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 278.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biovizBase.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:biovizBase.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings biovizBase_1.30.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/biovizBase.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.30.1’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
crunch-method 17.784 0.284 18.217
* 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/biovizBase.Rcheck/00check.log’
for details.
biovizBase.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL biovizBase
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘biovizBase’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/include/R_ext/RS.h:34,
from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/R_ext/RS.h:34:0,
from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/R_ext/RS.h:34,
from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/R_ext/RS.h:34:0,
from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/biovizBase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biovizBase)
biovizBase.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> 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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, 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,
rowMeans, rowSums, 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 object is masked from 'package:base':
expand.grid
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")'.
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
RUNIT TEST PROTOCOL -- Mon Apr 15 22:36:57 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
>
> proc.time()
user system elapsed
19.480 0.552 20.393
biovizBase.Rcheck/biovizBase-Ex.timings
| name | user | system | elapsed | |
| CRC | 0.004 | 0.000 | 0.002 | |
| GCcontent | 0.420 | 0.016 | 0.437 | |
| addStepping-method | 0.688 | 0.040 | 0.729 | |
| aes-utils | 0 | 0 | 0 | |
| colorBlindSafePal | 0 | 0 | 0 | |
| containLetters | 0.000 | 0.000 | 0.001 | |
| crc1.GeRL | 0.008 | 0.000 | 0.009 | |
| crunch-method | 17.784 | 0.284 | 18.217 | |
| darned_hg19_subset500 | 0.016 | 0.000 | 0.017 | |
| flatGrl | 0.248 | 0.000 | 0.251 | |
| genesymbol | 0.056 | 0.004 | 0.059 | |
| getBioColor | 0 | 0 | 0 | |
| getFormalNames | 0 | 0 | 0 | |
| getGaps | 1.384 | 0.000 | 1.385 | |
| getIdeoGR | 0.160 | 0.008 | 0.168 | |
| getIdeogram | 0 | 0 | 0 | |
| hg19Ideogram | 0.008 | 0.000 | 0.009 | |
| hg19IdeogramCyto | 0.012 | 0.000 | 0.010 | |
| ideo | 0.028 | 0.000 | 0.028 | |
| ideoCyto | 0.040 | 0.000 | 0.039 | |
| isIdeogram | 0.000 | 0.000 | 0.002 | |
| isMatchedWithModel | 0.308 | 0.004 | 0.335 | |
| isSimpleIdeogram | 0.016 | 0.000 | 0.017 | |
| maxGap-method | 0.368 | 0.000 | 0.368 | |
| pileupAsGRanges | 0 | 0 | 0 | |
| pileupGRangesAsVariantTable | 0 | 0 | 0 | |
| plotColorLegend | 0.000 | 0.000 | 0.002 | |
| scale | 0.200 | 0.000 | 0.201 | |
| showColor | 0 | 0 | 0 | |
| shrinkageFun-method | 0.144 | 0.000 | 0.147 | |
| splitByFacets-method | 0.264 | 0.000 | 0.263 | |
| strip_formula_dots | 0.004 | 0.000 | 0.001 | |
| subsetArgsByFormals | 0.000 | 0.000 | 0.001 | |
| transform | 3.032 | 0.048 | 3.082 | |
| transformGRangesForEvenSpace | 0.18 | 0.00 | 0.18 | |