BioC 3.1: CHECK report for ArrayExpressHTS on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpressHTS_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.18.0’
* 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 ‘ArrayExpressHTS’ can be installed ... [18s/18s] 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 loading without being on the library search path ... 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 Oct  8 22:33:25 2015 [AEHTS] Setting Options Step 1
Thu Oct  8 22:33:25 2015 [AEHTS] Setting Options Step 2
Thu Oct  8 22:33:25 2015 [AEHTS] Setting Options Step 3
Thu Oct  8 22:33:25 2015 [AEHTS] Found /usr/bin/fasta_formatter
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/fastx-toolkit-0.0.13 defined in the 'ArrayExpressHTS.fasta_formatter' option
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     cufflinks not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     samtools not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     bwa not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     mmseq not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     bam2hits not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     bowtie not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS]     tophat not found
Thu Oct  8 22:33:25 2015 [AEHTS] 
Thu Oct  8 22:33:25 2015 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct  8 22:33:25 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:33:25 2015 [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’
* 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 ... [8s/8s] 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-3.1-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.

* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/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’ [-Wimplicit-function-declaration]
     Rprintf("What?\n");
     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
     return(strcmp(k1->str, k2->str) == 0);
     ^
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’ [-Wimplicit-function-declaration]
     Rprintf("ID: %s, %d\n", k->str, k->length);
     ^
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’ [-Wimplicit-function-declaration]
         Rf_error("Fail to open BAM file %s\n", argv[1]);  
         ^
fltbam.c:125:17: 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:374:0,
                 from /usr/include/stdio.h:27,
                 from fltbam.c:1:
/usr/include/x86_64-linux-gnu/bits/string3.h:102:1: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
 __NTH (strcpy (char *__restrict __dest, const char *__restrict __src))
 ^
fltbam.c:126:17: 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-3.1-bioc/R/library/Rsamtools/include/samtools/bam.h:47:0,
                 from /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/sam.h:4,
                 from fltbam.c:2:
/usr/include/string.h:399:15: 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 [enabled by default]
 hashtable_iterator_value(struct hashtable_itr *i);
 ^
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
 hashtable_iterator_key(struct hashtable_itr *i);
 ^
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined [enabled by default]
 hashtable_iterator_value(struct hashtable_itr *i);
 ^
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
 hashtable_iterator_key(struct hashtable_itr *i);
 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c functions.c -o functions.o
functions.c: In function ‘getReadLength’:
functions.c:29:14: 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:30:14: 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:68:18: 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:69:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // read second line
                  ^
functions.c:70:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // read third line
                  ^
functions.c:71:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
             fgets(line, sizeof(line), infile); // and forth line
                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: Rle, subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: Rle, subseq
Thu Oct  8 22:31:57 2015 [AEHTS] Setting Options Step 1
Thu Oct  8 22:31:57 2015 [AEHTS] Setting Options Step 2
Thu Oct  8 22:31:57 2015 [AEHTS] Setting Options Step 3
Thu Oct  8 22:31:57 2015 [AEHTS] Found /usr/bin/fasta_formatter
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/fastx-toolkit-0.0.13 defined in the 'ArrayExpressHTS.fasta_formatter' option
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     cufflinks not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     samtools not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     bwa not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     mmseq not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     bam2hits not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     bowtie not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] *** WARNING ***
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS]     tophat not found
Thu Oct  8 22:31:57 2015 [AEHTS] 
Thu Oct  8 22:31:57 2015 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct  8 22:31:57 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct  8 22:31:57 2015 [AEHTS] 
* DONE (ArrayExpressHTS)

name	user	system	elapsed
ArrayExpressHTS	0.003	0.000	0.003
ArrayExpressHTSFastQ	0.006	0.000	0.006
isRCloud	0.001	0.000	0.001
package-options	0.002	0.000	0.002
prepareAnnotation	0.002	0.000	0.002
prepareReference	0.000	0.004	0.002
processing-options	0.001	0.000	0.001

BioC 3.1: CHECK report for ArrayExpressHTS on zin2

Summary

Command output