Angela Goncalves
| Snapshot Date: 2019-02-06 17:01:03 -0500 (Wed, 06 Feb 2019) |
| URL: https://git.bioconductor.org/packages/ArrayExpressHTS |
| Branch: master |
| Last Commit: 0db10b7 |
| Last Changed Date: 2019-01-04 13:08:26 -0500 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-02-07 14:00:13 -0500 (Thu, 07 Feb 2019).
| Package 71/1659 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ArrayExpressHTS 1.33.1 Angela Goncalves
| malbec2 | Linux (Ubuntu 18.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |||||||
| Package: ArrayExpressHTS |
| Version: 1.33.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpressHTS_1.33.1.tar.gz |
| StartedAt: 2019-02-06 23:32:06 -0500 (Wed, 06 Feb 2019) |
| EndedAt: 2019-02-06 23:37:37 -0500 (Wed, 06 Feb 2019) |
| EllapsedTime: 331.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ArrayExpressHTS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpressHTS_1.33.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.33.1’
* 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 ‘ArrayExpressHTS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Rsamtools’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
‘sampling’ ‘snow’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘assignPipelineOptions’ ‘createServerLog’ ‘getPipelineOption’
‘processOneProjectAlignment’ ‘processOneProjectAlnReport’
‘processOneProjectEstimation’ ‘processOneProjectRawReport’
‘setProjectData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Wed Feb 6 23:35:11 2019 [AEHTS] Setting Options Step 1
Wed Feb 6 23:35:11 2019 [AEHTS] Setting Options Step 2
Wed Feb 6 23:35:11 2019 [AEHTS] Setting Options Step 3
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] fasta_formatter not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] cufflinks not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] samtools not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] bwa not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] mmseq not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] bam2hits not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] bowtie not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] *** WARNING ***
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] tophat not found
Wed Feb 6 23:35:11 2019 [AEHTS]
Wed Feb 6 23:35:11 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Feb 6 23:35:11 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 23:35:11 2019 [AEHTS]
calculate_dustyScore: no visible global function definition for
‘srswor’
cleanupCluster: no visible global function definition for ‘stopCluster’
cleanupCluster: no visible global function definition for
‘cleanupClusters’
createServerLog: no visible global function definition for
‘sinkWorkerOutput’
cufflinks_to_granges: no visible global function definition for ‘Rle’
fastq_to_shortreadq: no visible global function definition for ‘subseq’
make_indexes_old: no visible global function definition for ‘subseq’
plot_readoccurence_cdf: no visible global function definition for
‘srswor’
prepareCluster: no visible global function definition for ‘makeCluster’
prepareCluster: no visible global function definition for
‘mergeClusters’
prepareCluster: no visible global function definition for
‘clusterApply’
prepareCluster: no visible global function definition for
‘clusterEvalQ’
readSDRF: no visible global function definition for
‘read.AnnotatedDataFrame’
runProjects: no visible global function definition for ‘clusterApply’
runProjects: no visible global function definition for ‘clusterEvalQ’
runProjects: no visible global function definition for ‘clusterApplyLB’
Undefined global functions or variables:
Rle cleanupClusters clusterApply clusterApplyLB clusterEvalQ
makeCluster mergeClusters read.AnnotatedDataFrame sinkWorkerOutput
srswor stopCluster subseq
* 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
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. 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
ArrayExpressHTS.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c addXS.c -o addXS.o
addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("What?\n");
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c fltbam.c -o fltbam.o
fltbam.c:40:19: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:77:25: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:40:28: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:77:39: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:45:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("ID: %s, %d\n", k->str, k->length);
^
fltbam.c:91:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration]
Rf_error("Fail to open BAM file %s\n", argv[1]);
^
fltbam.c:125:24: warning: passing 'unsigned char [50]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
strcpy(k->str, bam1_qname(line));
^˜˜˜˜˜
/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy'
__builtin___strcpy_chk (dest, src, __darwin_obsz (dest))
^˜˜˜
fltbam.c:126:36: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k->length = strlen(k->str);
^˜˜˜˜˜
/usr/include/string.h:82:28: note: passing argument to parameter here
size_t strlen(const char *);
^
In file included from fltbam.c:4:
./hashtable_itr.h:32:1: warning: inline function 'hashtable_iterator_key' is not defined [-Wundefined-inline]
hashtable_iterator_key(struct hashtable_itr *i);
^
fltbam.c:189:18: note: used here
kk = hashtable_iterator_key(itr);
^
In file included from fltbam.c:4:
./hashtable_itr.h:46:1: warning: inline function 'hashtable_iterator_value' is not defined [-Wundefined-inline]
hashtable_iterator_value(struct hashtable_itr *i);
^
fltbam.c:190:17: note: used here
v = hashtable_iterator_value(itr);
^
8 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c functions.c -o functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_itr.c -o hashtable_itr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -g -O2 -c hashtable_utility.c -o hashtable_utility.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 ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ArrayExpressHTS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’
Wed Feb 6 18:43:51 2019 [AEHTS] Setting Options Step 1
Wed Feb 6 18:43:51 2019 [AEHTS] Setting Options Step 2
Wed Feb 6 18:43:51 2019 [AEHTS] Setting Options Step 3
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] fasta_formatter not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] cufflinks not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] samtools not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] bwa not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] mmseq not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] bam2hits not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] bowtie not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] *** WARNING ***
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] tophat not found
Wed Feb 6 18:43:51 2019 [AEHTS]
Wed Feb 6 18:43:51 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Feb 6 18:43:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb 6 18:43:51 2019 [AEHTS]
* DONE (ArrayExpressHTS)
ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings
| name | user | system | elapsed | |
| ArrayExpressHTS | 0.004 | 0.001 | 0.004 | |
| ArrayExpressHTSFastQ | 0.009 | 0.001 | 0.010 | |
| isRCloud | 0.001 | 0.001 | 0.002 | |
| package-options | 0.001 | 0.001 | 0.002 | |
| prepareAnnotation | 0.002 | 0.001 | 0.002 | |
| prepareReference | 0.004 | 0.001 | 0.006 | |
| processing-options | 0.002 | 0.001 | 0.003 | |