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CHECK report for ArrayExpressHTS on malbec2

This page was generated on 2019-02-07 11:47:44 -0500 (Thu, 07 Feb 2019).

Package 71/1659HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.33.1
Angela Goncalves , Andrew Tikhonov
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)
malbec2 Linux (Ubuntu 18.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ArrayExpressHTS
Version: 1.33.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ArrayExpressHTS_1.33.1.tar.gz
StartedAt: 2019-02-07 00:17:43 -0500 (Thu, 07 Feb 2019)
EndedAt: 2019-02-07 00:21:53 -0500 (Thu, 07 Feb 2019)
EllapsedTime: 250.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ArrayExpressHTS_1.33.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* using platform: x86_64-pc-linux-gnu (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
Thu Feb  7 00:20:03 2019 [AEHTS] Setting Options Step 1
Thu Feb  7 00:20:03 2019 [AEHTS] Setting Options Step 2
Thu Feb  7 00:20:03 2019 [AEHTS] Setting Options Step 3
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     fasta_formatter not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     cufflinks not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     samtools not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     bwa not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     mmseq not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     bam2hits not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     bowtie not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] *** WARNING ***
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS]     tophat not found
Thu Feb  7 00:20:03 2019 [AEHTS] 
Thu Feb  7 00:20:03 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Feb  7 00:20:03 2019 [AEHTS] Use .Rprofile to make options persistent.
Thu Feb  7 00:20:03 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 ‘/home/biocbuild/bbs-3.9-bioc/R/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.

Installation output

ArrayExpressHTS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
     Rprintf("What?\n");
     ^˜˜˜˜˜˜
     dprintf
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:19: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness [-Wpointer-sign]
     return(strcmp(k1->str, k2->str) == 0);
                   ^˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/bam.h:47:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
                 from fltbam.c:2:
/usr/include/string.h:136:12: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
 extern int strcmp (const char *__s1, const char *__s2)
            ^˜˜˜˜˜
fltbam.c:40:28: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness [-Wpointer-sign]
     return(strcmp(k1->str, k2->str) == 0);
                            ^˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/bam.h:47:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
                 from fltbam.c:2:
/usr/include/string.h:136:12: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
 extern int strcmp (const char *__s1, const char *__s2)
            ^˜˜˜˜˜
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
     Rprintf("ID: %s, %d\n", k->str, k->length);
     ^˜˜˜˜˜˜
     dprintf
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’; did you mean ‘ferror’? [-Wimplicit-function-declaration]
         Rf_error("Fail to open BAM file %s\n", argv[1]);
         ^˜˜˜˜˜˜˜
         ferror
fltbam.c:125:24: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
                 strcpy(k->str, bam1_qname(line));
                        ^
In file included from /usr/include/features.h:424:0,
                 from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
                 from /usr/include/stdio.h:27,
                 from fltbam.c:1:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:88:1: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
 __NTH (strcpy (char *__restrict __dest, const char *__restrict __src))
 ^
fltbam.c:126:36: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
                 k->length = strlen(k->str);
                                    ^
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/bam.h:47:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
                 from fltbam.c:2:
/usr/include/string.h:384:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
 extern size_t strlen (const char *__s)
               ^˜˜˜˜˜
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
     struct key *k, *kk;
                     ^˜
In file included from fltbam.c:4:0:
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
 hashtable_iterator_value(struct hashtable_itr *i);
 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
 hashtable_iterator_key(struct hashtable_itr *i);
 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c functions.c -o functions.o
functions.c: In function ‘getReadLength’:
functions.c:29:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, sizeof(line), infile); // read first line and discard it
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:30:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, sizeof(line), infile); // read second line and check its length
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c: In function ‘checkQuality’:
functions.c:68:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // read first line and discard it
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:69:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // read second line
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:70:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // read third line
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
functions.c:71:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // and forth line
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.9-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 18:19:22 2019 [AEHTS] Setting Options Step 1
Wed Feb  6 18:19:22 2019 [AEHTS] Setting Options Step 2
Wed Feb  6 18:19:22 2019 [AEHTS] Setting Options Step 3
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     fasta_formatter not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     cufflinks not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     samtools not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     bwa not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     mmseq not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     bam2hits not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS]     bowtie not found
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:22 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Feb  6 18:19:22 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:22 2019 [AEHTS] 
Wed Feb  6 18:19:23 2019 [AEHTS] *** WARNING ***
Wed Feb  6 18:19:23 2019 [AEHTS] 
Wed Feb  6 18:19:23 2019 [AEHTS]     tophat not found
Wed Feb  6 18:19:23 2019 [AEHTS] 
Wed Feb  6 18:19:23 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Feb  6 18:19:23 2019 [AEHTS] Use .Rprofile to make options persistent.
Wed Feb  6 18:19:23 2019 [AEHTS] 
* DONE (ArrayExpressHTS)

Tests output

Example timings

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings

nameusersystemelapsed
ArrayExpressHTS0.0020.0000.003
ArrayExpressHTSFastQ0.0050.0000.005
isRCloud0.0000.0000.001
package-options0.0010.0000.001
prepareAnnotation0.0020.0000.002
prepareReference0.0030.0000.002
processing-options0.0020.0000.001