Ошибка tidyverse для зависимостей 'broom', 'modelr' недоступны

Я использую версию R 3.4.1 на x86_64-Redhat-Linux-GNU (64-разрядная версия) (экземпляр EC2). Я получаю следующую ошибку при попытке установить tidyverse, в которой говорится, что зависимости «broom» и «modelr» недоступны.

Я попытался установить пакет mnormt индивидуально, но это тоже не помогло.

P.S: Я убедился, что у меня на машине есть openssl, openssl-devel, libxml2, libxml2-devel, libcurl, libcurl-devel.

Stacktrace вставлен ниже:

install.packages("tidyverse", dependencies=TRUE)

Installing package into '/usr/lib64/R/library'
(as 'lib' is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                      2: Algeria [https]
 3: Australia (Canberra) [https]         4: Australia (Melbourne 1) [https]
 5: Australia (Melbourne 2) [https]      6: Australia (Perth) [https]
 7: Austria [https]                      8: Belgium (Ghent) [https]
 9: Brazil (PR) [https]                 10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]               12: Brazil (SP 2) [https]
13: Bulgaria [https]                    14: Chile 1 [https]
15: Chile 2 [https]                     16: China (Guangzhou) [https]
17: China (Lanzhou) [https]             18: China (Shanghai) [https]
19: Colombia (Cali) [https]             20: Czech Republic [https]
21: Denmark [https]                     22: East Asia [https]
23: Ecuador (Cuenca) [https]            24: Ecuador (Quito) [https]
25: Estonia [https]                     26: France (Lyon 1) [https]
27: France (Lyon 2) [https]             28: France (Marseille) [https]
29: France (Montpellier) [https]        30: France (Paris 2) [https]
31: Germany (Erlangen) [https]          32: Germany (G<U+00F6>ttingen) [https]
33: Germany (M<U+00FC>nster) [https]    34: Greece [https]
35: Iceland [https]                     36: Indonesia (Jakarta) [https]
37: Ireland [https]                     38: Italy (Padua) [https]
39: Japan (Tokyo) [https]               40: Japan (Yonezawa) [https]
41: Malaysia [https]                    42: Mexico (Mexico City) [https]
43: Norway [https]                      44: Philippines [https]
45: Serbia [https]                      46: Spain (A Coru<U+00F1>a) [https]
47: Spain (Madrid) [https]              48: Sweden [https]
49: Switzerland [https]                 50: Turkey (Denizli) [https]
51: Turkey (Mersin) [https]             52: UK (Bristol) [https]
53: UK (Cambridge) [https]              54: UK (London 1) [https]
55: USA (CA 1) [https]                  56: USA (IA) [https]
57: USA (KS) [https]                    58: USA (MI 1) [https]
59: USA (NY) [https]                    60: USA (OR) [https]
61: USA (TN) [https]                    62: USA (TX 1) [https]
63: Vietnam [https]                     64: (other mirrors)


Selection: 56
also installing the dependencies 'mnormt', 'psych', 'broom', 'modelr'

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/mnormt_1.5-5.tar.gz'
Content type 'application/x-gzip' length 37169 bytes (36 KB)
==================================================
downloaded 36 KB

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/psych_1.8.3.3.tar.gz'
Content type 'application/x-gzip' length 3500760 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/broom_0.4.4.tar.gz'
Content type 'application/x-gzip' length 1409358 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/modelr_0.1.1.tar.gz'
Content type 'application/x-gzip' length 83629 bytes (81 KB)
==================================================
downloaded 81 KB

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/tidyverse_1.2.1.tar.gz'
Content type 'application/x-gzip' length 61647 bytes (60 KB)
==================================================
downloaded 60 KB

During startup - Warning message:
Setting LC_CTYPE failed, using "C"
* installing *source* package 'mnormt' ...
** package 'mnormt' successfully unpacked and MD5 sums checked
** libs
gfortran -m64   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules  -c biv-nt.f -o biv-nt.o
f951: Warning: Nonexistent include directory '/usr/lib64/gfortran/modules' [-Wmissing-include-dirs]
biv-nt.f:371:11:

       hs = sign( one, dh - r*dk )
           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
biv-nt.f:372:11:

       ks = sign( one, dk - r*dh )
           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
gfortran -m64   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules  -c sadmvnt.f -o sadmvnt.o
f951: Warning: Nonexistent include directory '/usr/lib64/gfortran/modules' [-Wmissing-include-dirs]
sadmvnt.f:976:3:

  10      END DO
   1
Warning: Label 10 at (1) defined but not used
sadmvnt.f:80:15:

       INFORM = MVNNIT( N, CORREL, LOWER, UPPER, INFIN, INFIS, D, E )
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:217:38:

         IF ( MINCLS .LT. 0 ) SBRGNS = WORK(LENWRK)
                                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:275:21:

             RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:276:21:

             NWRGNS = NWRGNS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1274:24:

                POINTS = PONTRS(SUBTMP)
                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1275:24:

                POINTP = PONTRS(SUBTMP+1)
                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1283:21:

             POINTS = PONTRS(SUBTMP)
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1303:21:

             POINTS = PONTRS(SUBTMP)
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:324:15:

          TOP = PONTRS(1)
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:331:21:

             RGNCLS = RGNCLS*MESH(I)
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:336:18:

          RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN)
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1585:3:

  10      END DO
   1
Warning: Label 10 at (1) defined but not used
sadmvnt.f:1432:15:

       INFORM = MVTNIT( N, NU, CORREL, LOWER, UPPER, INFIN, INFIS, D, E )
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
sadmvnt.f:1661:0:

      &              /( 1 + BMIN**2/(NU+I-1) )**( (NU+I-2)/TWO )

Warning: 'bmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1658:0:

      &              /( 1 + AMIN**2/(NU+I-1) )**( (NU+I-2)/TWO )

Warning: 'amin' may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1127:0:

       INTEGER S, IXCHNG, LXCHNG, I, L

Warning: 'lxchng' may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:804:0:

       END

Warning: '__result_bvn' may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:762:0:

       DOUBLE PRECISION FUNCTION BVN ( LOWER, UPPER, INFIN, CORREL )

note: '__result_bvn' was declared here
sadmvnt.f:1046:0:

                   IF ( INFI(I) .EQ. 2 ) Y(I) = ( AMIN + BMIN )/2

Warning: 'bmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
sadmvnt.f:1046:0: Warning: 'amin' may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o mnormt.so biv-nt.o sadmvnt.o -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lquadmath
collect2: error: ld returned 1 exit status
make: *** [mnormt.so] Error 1
ERROR: compilation failed for package 'mnormt'
* removing '/usr/lib64/R/library/mnormt'
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
ERROR: dependency 'mnormt' is not available for package 'psych'
* removing '/usr/lib64/R/library/psych'
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
ERROR: dependency 'psych' is not available for package 'broom'
* removing '/usr/lib64/R/library/broom'
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
ERROR: dependency 'broom' is not available for package 'modelr'
* removing '/usr/lib64/R/library/modelr'
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
ERROR: dependencies 'broom', 'modelr' are not available for package 'tidyverse'
* removing '/usr/lib64/R/library/tidyverse'

The downloaded source packages are in
    '/tmp/RtmpukLj2J/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("tidyverse", dependencies = TRUE) :
  installation of package 'mnormt' had non-zero exit status
2: In install.packages("tidyverse", dependencies = TRUE) :
  installation of package 'psych' had non-zero exit status
3: In install.packages("tidyverse", dependencies = TRUE) :
  installation of package 'broom' had non-zero exit status
4: In install.packages("tidyverse", dependencies = TRUE) :
  installation of package 'modelr' had non-zero exit status
5: In install.packages("tidyverse", dependencies = TRUE) :
  installation of package 'tidyverse' had non-zero exit status

В сообщении об ошибке указано, что во время сборки mnormt компилятор не может найти пакеты lgfortran или lquadmath. Смотрите Сборка пакета R - при получении ошибки не удается найти lgfortran для потенциальных решений, хотя они могут незначительно отличаться в зависимости от версии Linux. Итог: вам нужно убедиться, что библиотеки lgfortran и lquadmath доступны компилятору gcc при сборке mnormt.

Len Greski 11.04.2018 13:28

Спасибо. Я сопоставил версию g ++, gcc и gfortran, но все еще вижу некоторые другие проблемы: подготовка пакета к отложенной загрузке Предупреждение: методы S3 '[.labelled', 'as.data.frame.labelled', 'as_factor.data.frame', ..] были объявлены в NAMESPACE, но не найдены Ошибка в library.dynam (lib, package, package.lib): общий объект 'haven.so' не найден ОШИБКА: не удалось выполнить отложенную загрузку для пакета 'tidyverse'

minion 11.04.2018 13:54
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