Comments (1)
I replied to this over at methylKit_discussion
On Sun, Jul 31, 2016 at 11:46 AM, Baffort [email protected] wrote:
Dear al2na,
I have installed the latest R and bioclite, but there were libtool error
when I were installing methykit package by using your install_github code
in R console. The detailed error information is attached below, thanks for
your help.Error information:
../libtool: line 5986: cd: :/ifshk1/BC_CANCER/03user/
lixiangchun/Software/INSTALL/hdf5-1.8.16/lib:/ifshk4/BC_
PUB/biosoft/PIPE_RD/Package/R-3.1.1/lib64/R/lib:/ifshk1/BC_
CANCER/03user/lixiangchun/Software/INSTALL/zlib-1.2.8/
lib:/ifshk1/BC_CANCER/03user/lixiangchun/Software/INSTALL/
bzip2-1.0.6/lib:/ifshk7/BC_RES/TECH/PMO/zhangbaifeng/
eDMR/xz/lib:/ifshk7/BC_RES/TECH/PMO/zhangbaifeng/eDMR/
pcre/lib:/ifshk7/BC_RES/TECH/PMO/zhangbaifeng/eDMR/pcre-8.39/curl/lib: No
such file or directory
libtool: link: cannot determine absolute directory name of
:/ifshk1/BC_CANCER/03user/lixiangchun/Software/INSTALL/
hdf5-1.8.16/lib:/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/R-
3.1.1/lib64/R/lib:/ifshk1/BC_CANCER/03user/lixiangchun/
Software/INSTALL/zlib-1.2.8/lib:/ifshk1/BC_CANCER/03user/
lixiangchun/Software/INSTALL/bzip2-1.0.6/lib:/ifshk7/BC_
RES/TECH/PMO/zhangbaifeng/eDMR/xz/lib:/ifshk7/BC_RES/
TECH/PMO/zhangbaifeng/eDMR/pcre/lib:/ifshk7/BC_RES/TECH/
PMO/zhangbaifeng/eDMR/pcre-8.39/curl/lib'
make[5]: *** [libgnu.la] Error 1
make[5]: Leaving directory/tmp/RtmpfLBspx/devtools7c1c1c4ee618/Rhtslib/src/htslib/lib'make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory /tmp/RtmpfLBspx/devtools7c1c1c4ee618/Rhtslib/src/htslib/lib'make[3]: *** [all] Error 2
make[3]: Leaving directory/tmp/RtmpfLBspx/devtools7c1c1c4ee618/Rhtslib/src/htslib/lib'make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory /tmp/RtmpfLBspx/devtools7c1c1c4ee618/Rhtslib/src/htslib'make[1]: *** [all] Error 2
make[1]: Leaving directory/tmp/RtmpfLBspx/devtools7c1c1c4ee618/Rhtslib/src/htslib'make: *** [htslib/libhts.la] Error 2
ERROR: compilation failed for package 'Rhtslib'
- removing '/ifshk7/BC_RES/TECH/PMO/zhangbaifeng/eDMR/R-3.3.1/library/Rhtslib'
Error: Command failed (1)—
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from methylkit.
Related Issues (20)
- Error reading in file HOT 3
- Interpreting the CpG pearson correlation plot HOT 3
- Data.frame error during differential methylation with covariate. HOT 7
- Illegal operation when opening BiocGenerics HOT 3
- error in getTargetAnnotationStats HOT 1
- The deep theory of calculateDiffMeth() function of MethylKit HOT 4
- MethylKit and Methylation Data from PacBio sequence HOT 2
- Fix bioc R-devel build issue HOT 3
- Typo in vignette
- percMethylation does not reach 100% HOT 3
- One question about DMR calling between single sample in one group versus replicated sample in another group HOT 4
- filter by chromosome HOT 1
- cannot find -lrtmp HOT 2
- MethylationStats shows one peak HOT 6
- error:Calls: calculateDiffMeth ... simplify2array -> mclapply -> lapply -> FUN -> mcfork HOT 2
- PCASamples options HOT 1
- tileMethylCounts(mrl_base, win.size=600,step.size=200,cov.bases = 4 HOT 1
- regioncounts lost some regions HOT 4
- Support for all context all types of methylation data
- NA values HOT 1
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