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al2na avatar al2na commented on August 25, 2024

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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