Entering edit mode
Erik Wright
▴
210
@erik-wright-4003
Last seen 9.6 years ago
Hello,
I am attempting to upgrade the Biostrings package on a linux box
running Ubuntu (10.04).
If I use:
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biostrings")
Afterwards the computer still has the same (presumably outdated)
version (2.14.12).
So I tried installing the development version from source with:
$ R CMD INSTALL './Biostrings_2.8.18.tar.gz'
and got the following error:
Error in isSingleNumber(length) : element 1 is empty;
the part of the args list of 'is.numeric' being evaluated was:
(x)
Then I tried install a release version from source using:
$ R CMD INSTALL './Biostrings_2.17.29.tar.gz'
and received a different error:
make: *** [MIndex_class.o] Error 1
ERROR: compilation failed for package ?Biostrings?
What am I doing wrong?
Thanks,
Erik
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.14.12 IRanges_1.4.16
loaded via a namespace (and not attached):
[1] Biobase_2.6.1
$ R CMD INSTALL './Biostrings_2.8.18.tar.gz'
* installing to library ?/R/x86_64-pc-linux-gnu-library/2.10?
* installing *source* package ?Biostrings? ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
ACtree_utils.c -o ACtree_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
IRanges_utils.c -o IRanges_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
MIndex_utils.c -o MIndex_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c XInteger.c
-o XInteger.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
XRaw_class.c -o XRaw_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
XRaw_utils.c -o XRaw_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
XString_class.c -o XString_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c bufutils.c
-o bufutils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
char_frequency.c -o char_frequency.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
char_translate.c -o char_translate.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c copy_seq.c
-o copy_seq.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
inject_code.c -o inject_code.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_TBdna.c -o match_TBdna.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
match_utils.c -o match_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
replace_locs.c -o replace_locs.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c
seqs_to_seqs.c -o seqs_to_seqs.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c utils.c -o
utils.o
gcc -std=gnu99 -shared -o Biostrings.so ACtree_utils.o IRanges_class.o
IRanges_utils.o MIndex_utils.o R_init_Biostrings.o SparseList_utils.o
XInteger.o XRaw_class.o XRaw_utils.o XStringSet_class.o
XString_class.o align_needwunsQS.o align_pairwiseAlignment.o
bufutils.o char_frequency.o char_translate.o copy_seq.o
find_palindromes.o inject_code.o match_BOC.o match_BOC2.o match_PWM.o
match_TBdna.o match_pattern.o match_pattern_boyermoore.o
match_pattern_shiftor.o match_reporting.o match_utils.o
pmatchPattern.o replace_locs.o seqs_to_seqs.o utils.o
-L/usr/lib64/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "start" in "Biostrings"
Creating a new generic function for "end" in "Biostrings"
Creating a new generic function for "as.data.frame" in "Biostrings"
Creating a new generic function for "update" in "Biostrings"
Creating a new generic function for "duplicated" in "Biostrings"
Creating a new generic function for "as.matrix" in "Biostrings"
Creating a new generic function for "append" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
Creating a new generic function for "as.list" in "Biostrings"
Creating a new generic function for "toString" in "Biostrings"
Error in isSingleNumber(length) : element 1 is empty;
the part of the args list of 'is.numeric' being evaluated was:
(x)
Error : unable to load R code in package 'Biostrings'
ERROR: lazy loading failed for package ?Biostrings?
* removing ?/R/x86_64-pc-linux-gnu-library/2.10/Biostrings?
* restoring previous ?/R/x86_64-pc-linux-gnu-library/2.10/Biostrings?
$ R CMD INSTALL './Biostrings_2.17.29.tar.gz'
* installing to library ?/R/x86_64-pc-linux-gnu-library/2.10?
* installing *source* package ?Biostrings? ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -I"/R/x86_64-pc-linux-gnu-
library/2.10/IRanges/include" -fpic -g -O2 -c BAB_class.c -o
BAB_class.o
gcc -std=gnu99 -I/usr/share/R/include -I"/R/x86_64-pc-linux-gnu-
library/2.10/IRanges/include" -fpic -g -O2 -c BitMatrix.c -o
BitMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -I"/R/x86_64-pc-linux-gnu-
library/2.10/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o
IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -I"/R/x86_64-pc-linux-gnu-
library/2.10/IRanges/include" -fpic -g -O2 -c MIndex_class.c -o
MIndex_class.o
MIndex_class.c: In function ?ByPos_MIndex_combine?:
MIndex_class.c:261: error: too many arguments to function
?IntAE_qsort?
MIndex_class.c:263: warning: implicit declaration of function
?new_INTEGER_from_IntAE?
MIndex_class.c:263: warning: assignment makes pointer from integer
without a cast
make: *** [MIndex_class.o] Error 1
ERROR: compilation failed for package ?Biostrings?
* removing ?/R/x86_64-pc-linux-gnu-library/2.10/Biostrings?
* restoring previous ?/R/x86_64-pc-linux-gnu-library/2.10/Biostrings?
