##############################################################################
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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_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.42.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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.
Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2
* 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 Oct 14 16:22:05 2021 [AEHTS] Setting Options Step 1
Thu Oct 14 16:22:05 2021 [AEHTS] Setting Options Step 2
Thu Oct 14 16:22:05 2021 [AEHTS] Setting Options Step 3
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     fasta_formatter not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     cufflinks not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     samtools not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     bwa not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     mmseq not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     bam2hits not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     bowtie not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] *** WARNING ***
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS]     tophat not found
Thu Oct 14 16:22:05 2021 [AEHTS] 
Thu Oct 14 16:22:05 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct 14 16:22:05 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 16:22:05 2021 [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’
getEnsemblAnnotation: no visible global function definition for
  ‘.path.package’
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:
  .path.package 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/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);
                  ^~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:25: note: passing argument to parameter '__s1' here
int      strcmp(const char *__s1, const char *__s2);
                            ^
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);
                           ^~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:77:43: note: passing argument to parameter '__s2' here
int      strcmp(const char *__s1, const char *__s2);
                                              ^
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:51:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
    Rprintf( "\tIndexes for %d mismatches of length %d: ", v->mm, v->length );
    ^
fltbam.c:70:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
    Rprintf( "Welcome, creating structures...\n" );
    ^
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));
                       ^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy'
                __builtin___strcpy_chk (dest, __VA_ARGS__, __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);
                                   ^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here
size_t   strlen(const char *__s);
                            ^
fltbam.c:215:9: 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:225:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration]
        Rf_error("Fail to open BAM file %s\n", argv[2]);
        ^
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);
                ^
12 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c functions.c -o functions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable_itr.c -o hashtable_itr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hashtable_utility.c -o hashtable_utility.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam.c -o sam.o
clang -mmacosx-version-min=10.13 -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 bam_plbuf.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o sam.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ArrayExpressHTS/00new/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 from temporary location
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’
Thu Oct 14 09:15:56 2021 [AEHTS] Setting Options Step 1
Thu Oct 14 09:15:56 2021 [AEHTS] Setting Options Step 2
Thu Oct 14 09:15:56 2021 [AEHTS] Setting Options Step 3
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     fasta_formatter not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     cufflinks not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     samtools not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     bwa not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     mmseq not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     bam2hits not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     bowtie not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS]     tophat not found
Thu Oct 14 09:15:56 2021 [AEHTS] 
Thu Oct 14 09:15:56 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct 14 09:15:56 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:15:56 2021 [AEHTS] 
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
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’
Thu Oct 14 09:16:08 2021 [AEHTS] Setting Options Step 1
Thu Oct 14 09:16:08 2021 [AEHTS] Setting Options Step 2
Thu Oct 14 09:16:08 2021 [AEHTS] Setting Options Step 3
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     fasta_formatter not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     cufflinks not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     samtools not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     bwa not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     mmseq not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     bam2hits not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     bowtie not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] *** WARNING ***
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS]     tophat not found
Thu Oct 14 09:16:08 2021 [AEHTS] 
Thu Oct 14 09:16:08 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct 14 09:16:08 2021 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 14 09:16:08 2021 [AEHTS] 
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)