sapFinder 1.12.0
Shaohang Xu , Bo Wen
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/sapFinder | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sapFinder_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sapFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sapFinder’ version ‘1.12.0’
* 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 ‘sapFinder’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
extdata 2.0Mb
* 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 loading without being on the library search path ... 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 ... NOTE
.spplot: no visible global function definition for ‘mtext’
.spplot: no visible global function definition for ‘axis’
.spplot: no visible global function definition for ‘points’
Sys.which2: no visible global function definition for ‘setNames’
Undefined global functions or variables:
axis mtext points setNames
Consider adding
importFrom("graphics", "axis", "mtext", "points")
importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 96626 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'sapFinder-Ex.Rout' 2>&1 < sapFinder-Ex.R
ERROR
Running examples in ‘sapFinder-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reportCreator
> ### Title: reportCreator
> ### Aliases: reportCreator
>
> ### ** Examples
>
> ## Step 1. Variation-associated database construction
> vcf <- system.file("extdata/sapFinder_test.vcf",
+ package="sapFinder")
> annotation <- system.file("extdata/sapFinder_test_ensGene.txt",
+ package="sapFinder")
> refseq <- system.file("extdata/sapFinder_test_ensGeneMrna.fa",
+ package="sapFinder")
> xref <- system.file("extdata/sapFinder_test_BioMart.Xref.txt",
+ package="sapFinder")
> outdir <- "db_dir"
> prefix <- "sapFinder_test"
> db.files <- dbCreator(vcf=vcf, annotation=annotation,
+ refseq=refseq, outdir=outdir,
+ prefix=prefix,xref=xref)
>
> ## Step 2. MS/MS searching
> mgf.path <- system.file("extdata/sapFinder_test.mgf",
+ package="sapFinder")
> fasta.path <- db.files[1]
> xml.path <- runTandem(spectra=mgf.path, fasta=fasta.path, outdir=".",
+ tol=10, tolu="ppm", itol=0.1, itolu="Daltons")
2017-04-15 07:51:14
Loading spectra
(mgf). loaded.
Spectra matching criteria = 331
Starting threads . started.
Computing models:
t
sequences modelled = 0 ks
Model refinement:
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
R(96626,0x7fff7a74c310) malloc: *** error for object 0x7feb6bc36018: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
* 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck/00check.log’
for details.
* installing *source* package ‘sapFinder’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c dataHandle.cpp -o dataHandle.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sapFinder.so dataHandle.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck/sapFinder/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sapFinder)