[R-br] Erro Java
Márcio Midon
marciomidon em gmail.com
Qua Mar 20 16:08:23 -03 2024
Ola grupo,
Fiz as instalações pedidas mas a única que o app não encontra é a
*llzma.* Instalei via Synaptic.
Segue novo log. em anexo.
Em 20/03/2024 08:20, Rodolfo Timoteo da Silva por (R-br) escreveu:
> Se você ler este log atentamente verificará que faltam várias coisas
> no seu ambiente:
>
> gfortran: not found
>
> libcurl was not found
>
>
> Adicionalmente:
>
> /usr/bin/ld: não foi possível localizar -lpcre2-8: Arquivo ou
> diretório inexistente
> /usr/bin/ld: não foi possível localizar -llzma: Arquivo ou diretório
> inexistente
> /usr/bin/ld: não foi possível localizar -lbz2: Arquivo ou diretório
> inexistente
>
>
> Você vai precisar pesquisar quais pacotes no seu ambiente são
> possíveis de corrigir estas ausências.
>
>
> Atenciosamente
>
> On 19/03/2024 21:35, Márcio Midon por (R-br) wrote:
>> Rodolfo...
>>
>> Resolvi uma parte mas tenho este log de erro ao instalar rjava e r5r.
>> (em anexo).
>>
>> Att
>>
>> Marcio Midon.
>>
>> Em 19/03/2024 16:10, Rodolfo Timoteo da Silva por (R-br) escreveu:
>>> Java problems:
>>>
>>> Dê uma olhada aqui para um norte (ou para desistir de vez).
>>>
>>> https://stackoverflow.com/questions/42562160/r-cmd-javareconf-not-finding-jni-h
>>>
>>>
>>> On 19/03/2024 14:54, Márcio Midon por (R-br) wrote:
>>>> conftest.c:1:10: fatal error: jni.h
>>>
>>>
>>> Atenciosamente
>>>
>>> _______________________________________________
>>> R-br mailing list
>>> R-br em listas.c3sl.ufpr.br
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>>> Leia o guia de postagem (http://www.leg.ufpr.br/r-br-guia) e forneça
>>> código mínimo reproduzível.
>>
>> _______________________________________________
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>> Leia o guia de postagem (http://www.leg.ufpr.br/r-br-guia) e forneça
>> código mínimo reproduzível.
> _______________________________________________
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> código mínimo reproduzível.
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> install.packages("rJava")
Installing package into ‘/home/analista/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
tentando a URL 'https://cloud.r-project.org/src/contrib/rJava_1.0-11.tar.gz'
Content type 'application/x-gzip' length 634103 bytes (619 KB)
==================================================
downloaded 619 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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 grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux'
java libs : '-L/usr/lib/jvm/jdk-22-oracle-x64/lib/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JVM will be loaded dynamically... no
checking whether JNI programs can be compiled... yes
checking whether JNI programs run... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether headless init is enabled... no
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/tmp/Rtmpr7CyYy/R.INSTALL448229fe5cea/rJava/jri)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for sys/types.h... (cached) yes
checking for sys/select.h... yes
checking Java version... 22
checking Java compatibility version (integer)... 22
checking whether actually works... no
checking whether javah was replaced by javac -h... yes
checking for target flags... -h . -target 1.8 -source 1.8
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rglue.c -o Rglue.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c arrayc.c -o arrayc.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callJNI.c -o callJNI.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callback.c -o callback.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fields.c -o fields.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c jri_glue.c -o jri_glue.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c loader.c -o loader.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c otables.c -o otables.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rJava.c -o rJava.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c registration.c -o registration.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rjstring.c -o rjstring.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tools.c -o tools.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o rjstring.o tools.o -L/usr/lib/jvm/jdk-22-oracle-x64/lib/server -ljvm -L/usr/lib/R/lib -lR
(cd ../jri && make)
make[1]: Entrando no diretório '/tmp/Rtmpr7CyYy/R.INSTALL448229fe5cea/rJava/jri'
make -C src JRI.jar
make[2]: Entrando no diretório '/tmp/Rtmpr7CyYy/R.INSTALL448229fe5cea/rJava/jri/src'
/usr/bin/javac -h . -target 1.8 -source 1.8 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
warning: [options] bootstrap class path is not set in conjunction with -source 8
not setting the bootstrap class path may lead to class files that cannot run on JDK 8
--release 8 is recommended instead of -source 8 -target 1.8 because it sets the bootstrap class path automatically
warning: [options] source value 8 is obsolete and will be removed in a future release
warning: [options] target value 8 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
../REXP.java:170: warning: [removal] finalize() in Object has been deprecated and marked for removal
protected void finalize() throws Throwable {
^
../REXP.java:175: warning: [removal] finalize() in Object has been deprecated and marked for removal
super.finalize();
^
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
6 warnings
if [ -n "" ]; then -d . -classpath . org.rosuda.JRI.Rengine; fi
gcc -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux
gcc -c -o rjstring.o rjstring.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -fpic -I/usr/lib/jvm/jdk-22-oracle-x64/include -I/usr/lib/jvm/jdk-22-oracle-x64/include/linux -I/usr/share/R/include -I/usr/share/R/include
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o rjstring.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -shared -L/usr/lib/jvm/jdk-22-oracle-x64/lib/server -ljvm -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n
/usr/bin/ld: não foi possível localizar -llzma: Arquivo ou diretório inexistente
collect2: error: ld returned 1 exit status
make[2]: Saindo do diretório '/tmp/Rtmpr7CyYy/R.INSTALL448229fe5cea/rJava/jri/src'
make[2]: *** [Makefile.all:40: libjri.so] Erro 1
make[1]: *** [Makefile.all:19: src/JRI.jar] Erro 2
make[1]: Saindo do diretório '/tmp/Rtmpr7CyYy/R.INSTALL448229fe5cea/rJava/jri'
make: *** [Makevars:14: jri] Erro 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/home/analista/R/x86_64-pc-linux-gnu-library/4.3/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpXHieEc/downloaded_packages’
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