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Last seen 10.2 years ago
Hi list,
I was try to install the flowStats package from Bioc and R stoped in
checking phase before compilation. Here goes the log error.
#######################################################
* installing *source* package ???XML??? ...
** package ???XML??? successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config...
/usr/local/programs/ccp4/ccp4-6.2.0/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 6, Patch 26 for 2.6.26
Located parser file
-I/usr/local/xtal/ccp4-6.2.0/include/libxml2/parser.h
Checking for 1.8: -I/usr/local/xtal/ccp4-6.2.0/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in
the default
directories.
ERROR: configuration failed for package ???XML???
* removing ???/home/ferreirafm/R/x86_64-pc-linux-gnu-
library/3.0/XML???
ERROR: dependency ???XML??? is not available for package
???flowWorkspace???
* removing ???/home/ferreirafm/R/x86_64-pc-linux-gnu-
library/3.0/flowWorkspace???
ERROR: dependency ???flowWorkspace??? is not available for package
???flowStats???
* removing ???/home/ferreirafm/R/x86_64-pc-linux-gnu-
library/3.0/flowStats???
The downloaded source packages are in
???/tmp/Rtmpur5nj8/downloaded_packages???
Mensagens de aviso perdidas:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ???XML??? had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ???flowWorkspace??? had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ???flowStats??? had non-zero exit status
#######################################################
Please, let me know if you need additional information.
Best,
Fred
-- output of sessionInfo():
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pt_BR.UTF-8 LC_COLLATE=pt_BR.UTF-8
[5] LC_MONETARY=pt_BR.UTF-8 LC_MESSAGES=pt_BR.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] flowCore_1.26.0 rrcov_1.3-3 pcaPP_1.9-49
[4] mvtnorm_0.9-9994 robustbase_0.9-7 Biobase_2.20.0
[7] BiocGenerics_0.6.0 BiocInstaller_1.10.1
loaded via a namespace (and not attached):
[1] feature_1.2.8 graph_1.38.0 ks_1.8.12 MASS_7.3-26
stats4_3.0.0
[6] tools_3.0.0
--
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