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This page was generated on 2021-10-23 14:05:53 -0400 (Sat, 23 Oct 2021).

CHECK results for ArrayExpressHTS on nebbiolo2

To the developers/maintainers of the ArrayExpressHTS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ArrayExpressHTS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 79/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.43.0  (landing page)
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/ArrayExpressHTS
git_branch: master
git_last_commit: 15a21c2
git_last_commit_date: 2021-05-19 11:48:38 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ArrayExpressHTS
Version: 1.43.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ArrayExpressHTS_1.43.0.tar.gz
StartedAt: 2021-10-22 19:06:30 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:10:03 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 213.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ArrayExpressHTS_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.43.0’
* 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 ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  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-3.14-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
Fri Oct 22 19:08:32 2021 [AEHTS] Setting Options Step 1
Fri Oct 22 19:08:32 2021 [AEHTS] Setting Options Step 2
Fri Oct 22 19:08:32 2021 [AEHTS] Setting Options Step 3
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     fasta_formatter not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     cufflinks not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     samtools not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     bwa not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     mmseq not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     bam2hits not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     bowtie not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] *** WARNING ***
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS]     tophat not found
Fri Oct 22 19:08:32 2021 [AEHTS] 
Fri Oct 22 19:08:32 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Oct 22 19:08:32 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 19:08:32 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 ‘/home/biocbuild/bbs-3.14-bioc/R/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.



Installation output

ArrayExpressHTS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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]
   42 |     Rprintf("What?\n");
      |     ^~~~~~~
      |     dprintf
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:17:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:14:19: note: length computed here
   14 |     int length1 = strlen(text1);
      |                   ^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:18:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:15:19: note: length computed here
   15 |     int length2 = strlen(text2);
      |                   ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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:40:21: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness [-Wpointer-sign]
   40 |     return(strcmp(k1->str, k2->str) == 0);
      |                   ~~^~~~~
      |                     |
      |                     unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from fltbam.c:2:
/usr/include/string.h:137:32: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
  137 | extern int strcmp (const char *__s1, const char *__s2)
      |                    ~~~~~~~~~~~~^~~~
fltbam.c:40:30: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness [-Wpointer-sign]
   40 |     return(strcmp(k1->str, k2->str) == 0);
      |                            ~~^~~~~
      |                              |
      |                              unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from fltbam.c:2:
/usr/include/string.h:137:50: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
  137 | 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]
   45 |     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]
   91 |         Rf_error("Fail to open BAM file %s\n", argv[1]);
      |         ^~~~~~~~
      |         ferror
fltbam.c:125:25: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
  125 |                 strcpy(k->str, bam1_qname(line));
      |                        ~^~~~~
      |                         |
      |                         unsigned char *
In file included from /usr/include/features.h:461,
                 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 *’
   88 | __NTH (strcpy (char *__restrict __dest, const char *__restrict __src))
      | ^~~~~
fltbam.c:126:37: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
  126 |                 k->length = strlen(k->str);
      |                                    ~^~~~~
      |                                     |
      |                                     unsigned char *
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/bam.h:45,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/sam.h:29,
                 from fltbam.c:2:
/usr/include/string.h:385:35: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
  385 | extern size_t strlen (const char *__s)
      |                       ~~~~~~~~~~~~^~~
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
   96 |     struct key *k, *kk;
      |                     ^~
In file included from fltbam.c:4:
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
   46 | hashtable_iterator_value(struct hashtable_itr *i);
      | ^~~~~~~~~~~~~~~~~~~~~~~~
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
   32 | hashtable_iterator_key(struct hashtable_itr *i);
      | ^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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]
   29 |         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]
   30 |         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]
   68 |             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]
   69 |             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]
   70 |             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]
   71 |             fgets(line, sizeof(line), infile); // and forth line
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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’
Fri Oct 22 16:14:45 2021 [AEHTS] Setting Options Step 1
Fri Oct 22 16:14:45 2021 [AEHTS] Setting Options Step 2
Fri Oct 22 16:14:45 2021 [AEHTS] Setting Options Step 3
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     fasta_formatter not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     cufflinks not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     samtools not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     bwa not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     mmseq not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     bam2hits not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     bowtie not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS]     tophat not found
Fri Oct 22 16:14:45 2021 [AEHTS] 
Fri Oct 22 16:14:45 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Oct 22 16:14:45 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:45 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’
Fri Oct 22 16:14:54 2021 [AEHTS] Setting Options Step 1
Fri Oct 22 16:14:54 2021 [AEHTS] Setting Options Step 2
Fri Oct 22 16:14:54 2021 [AEHTS] Setting Options Step 3
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     fasta_formatter not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     cufflinks not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     samtools not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     bwa not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     mmseq not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     bam2hits not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     bowtie not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] *** WARNING ***
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS]     tophat not found
Fri Oct 22 16:14:54 2021 [AEHTS] 
Fri Oct 22 16:14:54 2021 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Oct 22 16:14:54 2021 [AEHTS] Use .Rprofile to make options persistent.
Fri Oct 22 16:14:54 2021 [AEHTS] 
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)

Tests output


Example timings

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings

nameusersystemelapsed
ArrayExpressHTS0.0010.0000.001
ArrayExpressHTSFastQ0.0010.0000.002
isRCloud0.0010.0000.001
package-options0.0010.0000.001
prepareAnnotation0.0010.0000.001
prepareReference0.0010.0000.000
processing-options0.0000.0000.001