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CHECK report for ArrayExpressHTS on malbec2

This page was generated on 2019-10-16 11:59:51 -0400 (Wed, 16 Oct 2019).

Package 75/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.34.2
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ArrayExpressHTS
Branch: RELEASE_3_9
Last Commit: 7f2f1e6
Last Changed Date: 2019-06-25 21:04:52 -0400 (Tue, 25 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayExpressHTS
Version: 1.34.2
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_1.34.2.tar.gz
StartedAt: 2019-10-15 23:48:41 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:52:36 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 234.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 1

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_1.34.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.34.2’
* 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 ... WARNING
Found the following significant warnings:
  functions.c:29:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:30:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:68:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:69:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:70:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  functions.c:71:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/ArrayExpressHTS.Rcheck/00install.out’ for details.
* 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
Tue Oct 15 23:50:51 2019 [AEHTS] Setting Options Step 1
Tue Oct 15 23:50:51 2019 [AEHTS] Setting Options Step 2
Tue Oct 15 23:50:51 2019 [AEHTS] Setting Options Step 3
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     fasta_formatter not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     cufflinks not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     samtools not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     bwa not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     mmseq not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     bam2hits not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     bowtie not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] *** WARNING ***
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS]     tophat not found
Tue Oct 15 23:50:51 2019 [AEHTS] 
Tue Oct 15 23:50:51 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 15 23:50:51 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 23:50:51 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 ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (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: 1 WARNING, 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’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/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/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/sam.h:29,
                 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/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/sam.h:29,
                 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/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include/sam.h:29,
                 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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c sam.c -o sam.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/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 /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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’
Tue Oct 15 18:54:54 2019 [AEHTS] Setting Options Step 1
Tue Oct 15 18:54:54 2019 [AEHTS] Setting Options Step 2
Tue Oct 15 18:54:54 2019 [AEHTS] Setting Options Step 3
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     fasta_formatter not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     cufflinks not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     samtools not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     bwa not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     mmseq not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     bam2hits not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     bowtie not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS]     tophat not found
Tue Oct 15 18:54:54 2019 [AEHTS] 
Tue Oct 15 18:54:54 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 15 18:54:54 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:54:54 2019 [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’
Tue Oct 15 18:55:05 2019 [AEHTS] Setting Options Step 1
Tue Oct 15 18:55:05 2019 [AEHTS] Setting Options Step 2
Tue Oct 15 18:55:05 2019 [AEHTS] Setting Options Step 3
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     fasta_formatter not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     cufflinks not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     samtools not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     bwa not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     mmseq not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     bam2hits not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     bowtie not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] *** WARNING ***
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS]     tophat not found
Tue Oct 15 18:55:05 2019 [AEHTS] 
Tue Oct 15 18:55:05 2019 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct 15 18:55:05 2019 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct 15 18:55:05 2019 [AEHTS] 
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)

Tests output

Example timings

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings

nameusersystemelapsed
ArrayExpressHTS0.0030.0000.003
ArrayExpressHTSFastQ0.0060.0000.006
isRCloud0.0010.0000.001
package-options0.0010.0000.001
prepareAnnotation0.0010.0000.001
prepareReference0.0020.0000.002
processing-options0.0020.0000.002