linux install problems #21
Comments
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Your version of R is probably not configured with the correct C flags. Can you show me the full output of the compiler before the error happens? |
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I forgot to tell I am using "g++ (SUSE Linux) 8.1.1 20180614 [gcc-8-branch
revision 261584]"
Also please check the output for the "readxl" package...
Especially I am so curious about the following error:
./libxls/ole.h:174:8: error: unknown type name ‘ssize_t’
May be changing the version of the gcc can help?
I also got g++ 7.3.1
Here is the complete output below:
--------------------------------------------------------------------------------------------
install.packages("writexl")Installing package into
‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)trying URL
'https://cran.rstudio.com/src/contrib/writexl_1.0.tar.gz'Content type
'application/x-gzip' length 197041 bytes (192
KB)==================================================downloaded 192 KB
* installing *source* package ‘writexl’ ...** package ‘writexl’
successfully unpacked and MD5 sums checked** libsrm -f writexl.so
libxlsxwriter/libstatxlsxwriter.a write_xlsx.o libxlsxwriter/app.o
libxlsxwriter/format.o libxlsxwriter/theme.o libxlsxwriter/chart.o
libxlsxwriter/hash_table.o libxlsxwriter/utility.o
libxlsxwriter/content_types.o libxlsxwriter/packager.o
libxlsxwriter/workbook.o libxlsxwriter/core.o
libxlsxwriter/relationships.o libxlsxwriter/worksheet.o
libxlsxwriter/custom.o libxlsxwriter/shared_strings.o
libxlsxwriter/xmlwriter.o libxlsxwriter/drawing.o
libxlsxwriter/styles.o tmpfileplus/tmpfileplus.o minizip/ioapi.o
minizip/zip.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c write_xlsx.c -o write_xlsx.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/app.c -o libxlsxwriter/app.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/format.c -o
libxlsxwriter/format.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/theme.c -o
libxlsxwriter/theme.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/chart.c -o
libxlsxwriter/chart.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/hash_table.c -o
libxlsxwriter/hash_table.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/utility.c -o
libxlsxwriter/utility.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/content_types.c -o
libxlsxwriter/content_types.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/packager.c -o
libxlsxwriter/packager.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/workbook.c -o
libxlsxwriter/workbook.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/core.c -o libxlsxwriter/core.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/relationships.c -o
libxlsxwriter/relationships.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/worksheet.c -o
libxlsxwriter/worksheet.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/custom.c -o
libxlsxwriter/custom.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/shared_strings.c -o
libxlsxwriter/shared_strings.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/xmlwriter.c -o
libxlsxwriter/xmlwriter.olibxlsxwriter/xmlwriter.c: In function
‘_escape_attributes’:
libxlsxwriter/xmlwriter.c:156:17: warning: ‘strncat’ specified bound 5
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_AMP, sizeof(LXW_AMP) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c:160:17: warning: ‘strncat’ specified bound 4
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_LT, sizeof(LXW_LT) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c:164:17: warning: ‘strncat’ specified bound 4
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_GT, sizeof(LXW_GT) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c:168:17: warning: ‘strncat’ specified bound 6
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_QUOT, sizeof(LXW_QUOT) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c: In function ‘lxw_escape_data’:
libxlsxwriter/xmlwriter.c:198:17: warning: ‘strncat’ specified bound 5
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_AMP, sizeof(LXW_AMP) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c:202:17: warning: ‘strncat’ specified bound 4
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_LT, sizeof(LXW_LT) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libxlsxwriter/xmlwriter.c:206:17: warning: ‘strncat’ specified bound 4
equals source length [-Wstringop-overflow=]
strncat(p_encoded, LXW_GT, sizeof(LXW_GT) - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ccache
gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/drawing.c -o
libxlsxwriter/drawing.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c libxlsxwriter/styles.c -o
libxlsxwriter/styles.o
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iinclude -DNOCRYPT
-DNOUNCRYPT -I/usr/local/include -fvisibility=hidden -fpic -std=c99
-O3 -g0 -Wall -pipe -c tmpfileplus/tmpfileplus.c -o
tmpfileplus/tmpfileplus.otmpfileplus/tmpfileplus.c: In function
‘is_valid_dir’:
tmpfileplus/tmpfileplus.c:159:46: error: ‘S_IFDIR’ undeclared (first
use in this function); did you mean ‘S_ISDIR’?
if ((stat(path, &st) == 0) && (st.st_mode & S_IFDIR))
^~~~~~~
S_ISDIR
tmpfileplus/tmpfileplus.c:159:46: note: each undeclared identifier is
reported only once for each function it appears in
tmpfileplus/tmpfileplus.c: In function ‘mktempfile_internal’:
tmpfileplus/tmpfileplus.c:114:17: warning: implicit declaration of
function ‘fdopen’; did you mean ‘fopen’?
[-Wimplicit-function-declaration]
#define FDOPEN_ fdopen
^~~~~~
tmpfileplus/tmpfileplus.c:239:8: note: in expansion of macro ‘FDOPEN_’
fp = FDOPEN_(fd, "w+b");
^~~~~~~
tmpfileplus/tmpfileplus.c:239:6: warning: assignment to ‘FILE *’ {aka
‘struct _IO_FILE *’} from ‘int’ makes pointer from integer without a
cast [-Wint-conversion]
fp = FDOPEN_(fd, "w+b");
^
tmpfileplus/tmpfileplus.c: In function ‘tmpfileplus’:
tmpfileplus/tmpfileplus.c:290:18: error: ‘P_tmpdir’ undeclared (first
use in this function); did you mean ‘tmpdir’?
tempdirs[i++] = P_tmpdir;
^~~~~~~~
tmpdirmake: *** [/usr/lib64/R/etc/Makeconf:159:
tmpfileplus/tmpfileplus.o] Error 1ERROR: compilation failed for
package ‘writexl’* removing
‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/writexl’* restoring
previous ‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/writexl’Warning
in install.packages :
installation of package ‘writexl’ had non-zero exit statusThe
downloaded source packages are in
‘/tmp/Rtmp1tVhs6/downloaded_packages’
…--------------------------------------------------------------------------------------------
And also for the "readxl":
--------------------------------------------------------------------------------------------
install.packages("readxl")Installing package into
‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)trying URL
'https://cran.rstudio.com/src/contrib/readxl_1.1.0.tar.gz'Content type
'application/x-gzip' length 2036680 bytes (1.9
MB)==================================================downloaded 1.9 MB
* installing *source* package ‘readxl’ ...** package ‘readxl’
successfully unpacked and MD5 sums checked** libsccache g++-8
-I"/usr/lib64/R/include" -DNDEBUG -Iunix -I. -fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -g -O3 -Wall -pipe -c RcppExports.cpp -o
RcppExports.o
ccache g++-8 -I"/usr/lib64/R/include" -DNDEBUG -Iunix -I.
-fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -g -O3 -Wall -pipe -c XlsWorkBook.cpp -o
XlsWorkBook.oXlsWorkBook.cpp:4: warning: ignoring #pragma clang
diagnostic [-Wunknown-pragmas]
# pragma clang diagnostic ignored "-Wc99-extensions"
In file included from XlsWorkBook.h:6,
from XlsWorkBook.cpp:6:
ColSpec.h:5: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
# pragma clang diagnostic ignored "-Wc99-extensions"
ccache g++-8 -I"/usr/lib64/R/include" -DNDEBUG -Iunix -I.
-fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -g -O3 -Wall -pipe -c XlsWorkSheet.cpp
-o XlsWorkSheet.oIn file included from XlsWorkSheet.cpp:3:
ColSpec.h:5: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
# pragma clang diagnostic ignored "-Wc99-extensions"
ccache g++-8 -I"/usr/lib64/R/include" -DNDEBUG -Iunix -I.
-fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -g -O3 -Wall -pipe -c XlsxWorkBook.cpp
-o XlsxWorkBook.oIn file included from XlsxWorkBook.h:6,
from XlsxWorkBook.cpp:2:
ColSpec.h:5: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
# pragma clang diagnostic ignored "-Wc99-extensions"
ccache g++-8 -I"/usr/lib64/R/include" -DNDEBUG -Iunix -I.
-fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -g -O3 -Wall -pipe -c XlsxWorkSheet.cpp
-o XlsxWorkSheet.oIn file included from XlsxWorkSheet.cpp:2:
ColSpec.h:5: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
# pragma clang diagnostic ignored "-Wc99-extensions"
ccache gcc-8 -I"/usr/lib64/R/include" -DNDEBUG -Iunix -I.
-fvisibility=hidden
-I"/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/Rcpp/include"
-I/usr/local/include -fpic -std=c99 -O3 -g0 -Wall -pipe -c
endian.c -o endian.oIn file included from ./libxls/xlsstruct.h:40,
from libxls/endian.h:30,
from endian.c:33:
./libxls/ole.h:174:8: error: unknown type name ‘ssize_t’
extern ssize_t ole2_read(void* buf,size_t size,size_t count,OLE2Stream* olest);
^~~~~~~make: *** [/usr/lib64/R/etc/Makeconf:159: endian.o]
Error 1ERROR: compilation failed for package ‘readxl’* removing
‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/readxl’* restoring
previous ‘/home/kemal/R/x86_64-suse-linux-gnu-library/3.5/readxl’Warning
in install.packages :
installation of package ‘readxl’ had non-zero exit statusThe
downloaded source packages are in
‘/tmp/Rtmp1tVhs6/downloaded_packages’
--------------------------------------------------------------------------------------------
On Mon, Jun 25, 2018 at 10:32 PM, Jeroen Ooms ***@***.***> wrote:
Your version of R is probably not configured with the correct C flags. Can
you show me the full output of the compiler before the error happens?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#21 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ABGzkxRjDsophqdQvPSraplZFwCFLcX8ks5uATrogaJpZM4U2eiJ>
.
--
Kemal
If you only at least one time today, you have made God smile, then the day
is a gain for you.
Otherwise keep on smiling, tomorrow is another day, another chance!!!
Pax et Bonum
|
|
Looks like the problem first appears here: This macro should be defined by your operating system in |
|
I got that file in:
/usr/include/sys/stat.h
…On Mon, Jun 25, 2018 at 11:03 PM, Jeroen Ooms ***@***.***> wrote:
Looks like the problem first appears here:
tmpfileplus/tmpfileplus.c:159:46: error: ‘S_IFDIR’ undeclared (first
use in this function); did you mean ‘S_ISDIR’?
if ((stat(path, &st) == 0) && (st.st_mode & S_IFDIR))
^~~~~~~
S_ISDIR
This macro should be defined by your operating system in #include
<sys/stat.h>.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#21 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ABGzk0-7aomraPLIRe_JuX39sMFEWGzzks5uAUIDgaJpZM4U2eiJ>
.
--
Kemal
If you only at least one time today, you have made God smile, then the day
is a gain for you.
Otherwise keep on smiling, tomorrow is another day, another chance!!!
Pax et Bonum
|
|
Well it looks like there is something wrong with it. Which distribution is this? |
|
opensuse tumbleweed 64 bit
…On Mon, Jun 25, 2018 at 11:16 PM, Jeroen Ooms ***@***.***> wrote:
Well it looks like there is something wrong with it. Which distribution is
this?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#21 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ABGzk3mTS_R0QtLz_7p4Iad5T5rMIvNHks5uAUUhgaJpZM4U2eiJ>
.
--
Kemal
If you only at least one time today, you have made God smile, then the day
is a gain for you.
Otherwise keep on smiling, tomorrow is another day, another chance!!!
Pax et Bonum
|
|
Does this problem still exist? I think it is a bug in your linux installation. |
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Thanks for your interest! |
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I have just installed the package in tumbleweed in docker and it works fine. I think it is a bug in your linux installation. # Run docker
docker run -i -t opensuse/tumbleweed bash
# Run in container:
zypper update
zypper install R-devel gcc zlib-devel
#install writexl
R -e 'install.packages("writexl", repos = "https://cloud.r-project.org")' |
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Hello,
Using 64 bit linux and Rstudio.
R is version 3.5
I get error when I try to install writexl
Any idea why am I getting this error:
...
tmpfileplus/tmpfileplus.c:239:6: warning: assignment to ‘FILE *’ {aka ‘struct IO_FILE *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
fp = FDOPEN(fd, "w+b");
^
tmpfileplus/tmpfileplus.c: In function ‘tmpfileplus’:
tmpfileplus/tmpfileplus.c:290:18: error: ‘P_tmpdir’ undeclared (first use in this function); did you mean ‘tmpdir’?
tempdirs[i++] = P_tmpdir;
^~~~~~~~
tmpdir
make: *** [/usr/lib64/R/etc/Makeconf:159: tmpfileplus/tmpfileplus.o] Error 1
ERROR: compilation failed for package ‘writexl’
...
Any help welcome.
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