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INSTALL report for ArrayExpressHTS on malbec1

This page was generated on 2020-08-11 11:18:11 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ArrayExpressHTS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 76/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.39.1
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/ArrayExpressHTS
Branch: master
Last Commit: 6fd6f54
Last Changed Date: 2020-07-14 16:00:40 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayExpressHTS
Version: 1.39.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
StartedAt: 2020-08-10 16:50:00 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 16:50:57 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 57.1 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/Rhtslib/include/bam.h:45:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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’
Mon Aug 10 16:50:42 2020 [AEHTS] Setting Options Step 1
Mon Aug 10 16:50:42 2020 [AEHTS] Setting Options Step 2
Mon Aug 10 16:50:42 2020 [AEHTS] Setting Options Step 3
Mon Aug 10 16:50:42 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS]     fasta_formatter not found
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Mon Aug 10 16:50:42 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS]     cufflinks not found
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Aug 10 16:50:42 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS]     samtools not found
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Aug 10 16:50:42 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS]     bwa not found
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Aug 10 16:50:42 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS]     mmseq not found
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:42 2020 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Aug 10 16:50:42 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:42 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS]     bam2hits not found
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Aug 10 16:50:43 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS]     bowtie not found
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Aug 10 16:50:43 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS]     tophat not found
Mon Aug 10 16:50:43 2020 [AEHTS] 
Mon Aug 10 16:50:43 2020 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Aug 10 16:50:43 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:43 2020 [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’
Mon Aug 10 16:50:56 2020 [AEHTS] Setting Options Step 1
Mon Aug 10 16:50:56 2020 [AEHTS] Setting Options Step 2
Mon Aug 10 16:50:56 2020 [AEHTS] Setting Options Step 3
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     fasta_formatter not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     cufflinks not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     samtools not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     bwa not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     mmseq not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     bam2hits not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS]     bowtie not found
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:56 2020 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Aug 10 16:50:56 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:56 2020 [AEHTS] 
Mon Aug 10 16:50:57 2020 [AEHTS] *** WARNING ***
Mon Aug 10 16:50:57 2020 [AEHTS] 
Mon Aug 10 16:50:57 2020 [AEHTS]     tophat not found
Mon Aug 10 16:50:57 2020 [AEHTS] 
Mon Aug 10 16:50:57 2020 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Aug 10 16:50:57 2020 [AEHTS] Use .Rprofile to make options persistent.
Mon Aug 10 16:50:57 2020 [AEHTS] 
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpressHTS)