Rserve with R version 4.0

KNIME Extensions
1

Hi
I recently upgraded my R version from 3.5 to 4 and my knime version is 4.1.3. I start to have issue with Rserve. My current Rserve version is defaulted to
packageVersion(“Rserve”)
[1] ‘1.7.3.1’

I have searched the forum for solutions and tried the command
install.packages(‘Rserve’,“http://rforge.net/",type="source”)
Here is what I got

Installing package into ‘/Users/xxx/Library/R/4.0/library’
(as ‘lib’ is unspecified)
trying URL 'http://rforge.net/src/contrib/Rserve_1.8-6.tar.gz'
Content type 'application/x-gzip' length 498657 bytes (486 KB)
downloaded 486 KB

* installing *source* package ‘Rserve’ ...
** using staged installation
checking whether to compile the server... yes
checking whether to compile the client... no
checking for gcc... /usr/local/Cellar/gcc/8.3.0/bin/gcc-8
checking whether the C compiler works... no
configure: error: in `/private/var/folders/tm/gsxql1_j2zz23kt4c858p2mj_jz7py/T/Rtmp7hBM6C/R.INSTALL1ca76c335c07/Rserve':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘Rserve’
* removing ‘/Users/xxx/Library/R/4.0/library/Rserve’
* restoring previous ‘/Users/xxx/Library/R/4.0/library/Rserve’
Warning in install.packages :
  installation of package ‘Rserve’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/tm/gsxql1_j2zz23kt4c858p2mj_jz7py/T/Rtmp80cy0F/downloaded_packages’

Is there any other way to solve the issue?

Thank you in advance!

2

You can follow the instructions for installing R on Mac

https://docs.knime.com/2019-12/r_installation_guide/index.html

1 Like
3

I have followed the instruction using the shell script but the same issue persists.

4

You should check if you followed all steps and maybe reinstall the additional software necessary like clang and Fortran.

And you should use the script (https://bitbucket.org/KNIME/knime-r/src/master/org.knime.r/scripts/) and maybe install r version 4.0.1 when you are at it.

Do not forget to make the script executable.

On one occasion I had to install RServe from a downloaded file instead of from the internet directly (which makes no sense but still …).

5

@yuqiwang,

is this the whole output? Currently, I’d assume that your C-compiler causes the problems. Could you try to update brew (if you’re using it) as well as x-code and tests if that solves your problem?

Best
Mark

6

I basically reinstalled my xcode and updated brew… it doesn’t solve my issue. I even downgraded my R version to 3.6.3 and the problems still persists.

7

I have updated my gcc and fortran, re-installed xcode as well… not sure what is going on here. The shell script was executable, also had the 1.8-6 on my local for local install… no luck :frowning:

8

Could you elaborate what happens if you try to run the .sh script provided by KNIME? I have used this on two different Mac machines with success. You will be prompted to enter your password on two occasions.

9

I was only prompted once and here is what the terminal output after I ran the script
HQSML-152108:Desktop ywang203$ ./mac_10.14_or_higher.sh
INFO >>> Checking if Homebrew package manager is installed …
INFO >>> |- Homebrew package manager is already installed! Type ‘brew --version’ to get more details.
INFO >>> Checking if R is installed …
INFO >>> |- R is already installed! Type ‘R --version’ to get more details.
Password:
INFO >>> Installing R package “ggplot2”

R version 4.0.1 (2020-06-06) – “See Things Now”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.

Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

install.packages(“ggplot2”, repos = c(“https://cloud.r-project.org/”, “http://rforge.net”))
Installing package into ‘/Users/ywang203/Library/R/4.0/library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ps’, ‘processx’, ‘callr’, ‘prettyunits’, ‘backports’, ‘desc’, ‘pkgbuild’, ‘rprojroot’, ‘rstudioapi’, ‘evaluate’, ‘pkgload’, ‘praise’, ‘colorspace’, ‘testthat’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘viridisLite’, ‘gtable’, ‘isoband’, ‘scales’, ‘withr’

Warning: unable to access index for repository http://rforge.net/bin/macosx/contrib/4.0:
cannot open URL ‘http://rforge.net/bin/macosx/contrib/4.0/PACKAGES’

There is a binary version available but the source version is later:
binary source needs_compilation
evaluate 0.14 0.14.1 TRUE

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/ps_1.3.3.tgz’
Content type ‘application/x-gzip’ length 216748 bytes (211 KB)

downloaded 211 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/processx_3.4.2.tgz’
Content type ‘application/x-gzip’ length 252447 bytes (246 KB)

downloaded 246 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/callr_3.4.3.tgz’
Content type ‘application/x-gzip’ length 389420 bytes (380 KB)

downloaded 380 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/prettyunits_1.1.1.tgz’
Content type ‘application/x-gzip’ length 34627 bytes (33 KB)

downloaded 33 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/backports_1.1.7.tgz’
Content type ‘application/x-gzip’ length 69131 bytes (67 KB)

downloaded 67 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/desc_1.2.0.tgz’
Content type ‘application/x-gzip’ length 285956 bytes (279 KB)

downloaded 279 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/pkgbuild_1.0.8.tgz’
Content type ‘application/x-gzip’ length 135747 bytes (132 KB)

downloaded 132 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/rprojroot_1.3-2.tgz’
Content type ‘application/x-gzip’ length 78692 bytes (76 KB)

downloaded 76 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/rstudioapi_0.11.tgz’
Content type ‘application/x-gzip’ length 256053 bytes (250 KB)

downloaded 250 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/pkgload_1.1.0.tgz’
Content type ‘application/x-gzip’ length 150025 bytes (146 KB)

downloaded 146 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/praise_1.0.0.tgz’
Content type ‘application/x-gzip’ length 16129 bytes (15 KB)

downloaded 15 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/colorspace_1.4-1.tgz’
Content type ‘application/x-gzip’ length 2566663 bytes (2.4 MB)

downloaded 2.4 MB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/testthat_2.3.2.tgz’
Content type ‘application/x-gzip’ length 2367904 bytes (2.3 MB)

downloaded 2.3 MB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/farver_2.0.3.tgz’
Content type ‘application/x-gzip’ length 1829228 bytes (1.7 MB)

downloaded 1.7 MB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/labeling_0.3.tgz’
Content type ‘application/x-gzip’ length 60014 bytes (58 KB)

downloaded 58 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/munsell_0.5.0.tgz’
Content type ‘application/x-gzip’ length 240853 bytes (235 KB)

downloaded 235 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/RColorBrewer_1.1-2.tgz’
Content type ‘application/x-gzip’ length 52881 bytes (51 KB)

downloaded 51 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/viridisLite_0.3.0.tgz’
Content type ‘application/x-gzip’ length 56992 bytes (55 KB)

downloaded 55 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/gtable_0.3.0.tgz’
Content type ‘application/x-gzip’ length 431366 bytes (421 KB)

downloaded 421 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/isoband_0.2.1.tgz’
Content type ‘application/x-gzip’ length 4275585 bytes (4.1 MB)

downloaded 4.1 MB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/scales_1.1.1.tgz’
Content type ‘application/x-gzip’ length 551021 bytes (538 KB)

downloaded 538 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/withr_2.2.0.tgz’
Content type ‘application/x-gzip’ length 203935 bytes (199 KB)

downloaded 199 KB

trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/ggplot2_3.3.1.tgz’
Content type ‘application/x-gzip’ length 4016342 bytes (3.8 MB)

downloaded 3.8 MB

The downloaded binary packages are in
/tmp/RtmpydGm2A/downloaded_packages
installing the source package ‘evaluate’

trying URL ‘http://rforge.net/src/contrib/evaluate_0.14.1.tar.gz’
Content type ‘application/x-gzip’ length 21492 bytes (20 KB)

downloaded 20 KB

  • installing source package ‘evaluate’ …
    ** using staged installation
    ** R
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (evaluate)

The downloaded source packages are in
‘/private/tmp/RtmpydGm2A/downloaded_packages’

INFO >>> Installing R package “data.table”

R version 4.0.1 (2020-06-06) – “See Things Now”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.

Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

install.packages(“data.table”, repos = c(“https://cloud.r-project.org/”, “http://rforge.net”))
Installing package into ‘/Users/ywang203/Library/R/4.0/library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://rforge.net/bin/macosx/contrib/4.0:
cannot open URL ‘http://rforge.net/bin/macosx/contrib/4.0/PACKAGES’
trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/data.table_1.12.8.tgz’
Content type ‘application/x-gzip’ length 2070859 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

The downloaded binary packages are in
/tmp/RtmpPpkStU/downloaded_packages

INFO >>> Installing R package “pmml”

R version 4.0.1 (2020-06-06) – “See Things Now”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.

Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

install.packages(“pmml”, repos = c(“https://cloud.r-project.org/”, “http://rforge.net”))
Installing package into ‘/Users/ywang203/Library/R/4.0/library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://rforge.net/bin/macosx/contrib/4.0:
cannot open URL ‘http://rforge.net/bin/macosx/contrib/4.0/PACKAGES’
trying URL ‘https://cloud.r-project.org/bin/macosx/contrib/4.0/pmml_2.3.1.tgz’
Content type ‘application/x-gzip’ length 657459 bytes (642 KB)
==================================================
downloaded 642 KB

The downloaded binary packages are in
/tmp/RtmpfkHqav/downloaded_packages

INFO >>> Installing R package “Cairo”

R version 4.0.1 (2020-06-06) – “See Things Now”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.

Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

install.packages(“Cairo”, repos = c(“https://cloud.r-project.org/”, “http://rforge.net”))
Installing package into ‘/Users/ywang203/Library/R/4.0/library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://rforge.net/bin/macosx/contrib/4.0:
cannot open URL ‘http://rforge.net/bin/macosx/contrib/4.0/PACKAGES’

There is a binary version available but the source version is later:
binary source needs_compilation
Cairo 1.5-12 1.5-13 TRUE

installing the source package ‘Cairo’

trying URL ‘http://rforge.net/src/contrib/Cairo_1.5-13.tar.gz’
Content type ‘application/x-gzip’ length 85614 bytes (83 KB)

downloaded 83 KB

  • installing source package ‘Cairo’ …
    ** using staged installation
    checking for gcc… /usr/local/Cellar/gcc/8.3.0/bin/gcc-8
    checking whether the C compiler works… no
    configure: error: in /private/tmp/RtmpyqSuDq/R.INSTALL42646bc3dd29/Cairo': configure: error: C compiler cannot create executables See config.log’ for more details
    ERROR: configuration failed for package ‘Cairo’
  • removing ‘/Users/ywang203/Library/R/4.0/library/Cairo’

The downloaded source packages are in
‘/private/tmp/Rtmpm42z6s/downloaded_packages’
Warning message:
In install.packages(“Cairo”, repos = c(“https://cloud.r-project.org/”, :
installation of package ‘Cairo’ had non-zero exit status

INFO >>> Installing R package “Rserve”
INFO >>> |- Installating required system package openssl …
Updating Homebrew…
==> Auto-updated Homebrew!
Updated 2 taps (homebrew/core and homebrew/cask).
==> Updated Formulae
abcmidi certbot cython doctl jc prestodb
==> Updated Casks
aircall bettertouchtool cacher cleanmymac netbeans prepros securityspy wondershare-filmora

Warning: openssl@1.1 1.1.1g is already installed and up-to-date
To reinstall 1.1.1g, run brew reinstall openssl@1.1
Error: Failure while executing; find /usr/local/Cellar/openssl@1.1/1.1.1g -not -type d -print exited with 127. Here’s the output:
/usr/local/Cellar/openssl@1.1/1.1.1g/INSTALL_RECEIPT.json
/usr/local/Cellar/openssl@1.1/1.1.1g/LICENSE
/usr/local/Cellar/openssl@1.1/1.1.1g/bin/c_rehash
/usr/local/Cellar/openssl@1.1/1.1.1g/bin/openssl
/usr/local/Cellar/openssl@1.1/1.1.1g/.brew/openssl@1.1.rb
/usr/local/Cellar/openssl@1.1/1.1.1g/AUTHORS
/usr/local/Cellar/openssl@1.1/1.1.1g/CHANGES
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pem2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/kdf.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pem.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/asyncerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/md2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ssl3.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ossl_typ.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/dtls1.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/err.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/bn.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/blowfish.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/cms.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/engine.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/conf_api.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/x509.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/asn1_mac.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/objectserr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/cmserr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ui.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/sha.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/symhacks.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/asn1.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/bioerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/opensslconf.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/bio.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rc2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/dh.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/x509v3.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/conf.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rand_drbg.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/md5.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pemerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/x509_vfy.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/txt_db.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/comperr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/cterr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/safestack.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ecdsa.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/sslerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rc5.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/uierr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/x509v3err.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/objects.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pkcs12.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/crypto.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/opensslv.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/evperr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pkcs7.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/obj_mac.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ct.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/async.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/buffer.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ssl.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/srp.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/camellia.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/dherr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/evp.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/e_os2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/md4.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/hmac.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/aes.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/engineerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/comp.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pkcs12err.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/cast.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rc4.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/stack.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/des.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ocsp.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ec.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ecdh.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rand.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ecerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ts.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/cryptoerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/storeerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/buffererr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/seed.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/modes.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ssl2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/tserr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rsa.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ripemd.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/whrlpool.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/tls1.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/rsaerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/randerr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/mdc2.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/ocsperr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/x509err.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/pkcs7err.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/dsa.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/kdferr.h
/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/srtp.h
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/usr/local/Cellar/openssl@1.1/1.1.1g/include/openssl/store.h
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/usr/local/Cellar/openssl@1.1/1.1.1g/README
/usr/local/Cellar/openssl@1.1/1.1.1g/NEWS
/usr/local/Cellar/openssl@1.1/1.1.1g/lib/libcrypto.a
/usr/local/Cellar/openssl@1.1/1.1.1g/lib/pkgconfig/openssl.pc
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/usr/local/Cellar/openssl@1.1/1.1.1g/lib/libcrypto.dylib
/usr/local/Cellar/openssl@1.1/1.1.1g/lib/libssl.a
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/usr/local/Cellar/openssl@1.1/1.1.1g/lib/libcrypto.1.1.dylib
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/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/misc/tsget.pl
/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/misc/CA.pl
/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/ct_log_list.cnf
/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/openssl.cnf.dist
/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/openssl.cnf
/usr/local/Cellar/openssl@1.1/1.1.1g/.bottle/etc/openssl@1.1/ct_log_list.cnf.dist
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/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man5/x509v3_config.5ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/NAMING_AUTHORITY_set0_authorityText.3ssl
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/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_get0_peername.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/i2d_DSAPrivateKey.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/sk_TYPE_unshift.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OCSP_check_validity.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/ENGINE_ctrl_cmd.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/HMAC_CTX_reset.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_SignInit.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OCSP_RESPDATA_new.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_PUBKEY_get0.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_get_peer_signature_type_nid.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_security_bits.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_set_cipher_list.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_STORE_CTX_get_cleanup.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/PKCS7_new.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_STORE_CTX_verify_cb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_STORE_CTX_set_cert.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/RSA_public_decrypt.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BIO_get_mem_data.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DSA_print_fp.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_is_prime_fasttest_ex.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/ASYNC_WAIT_CTX_get_all_fds.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_enc_null.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_CTX_get_verify_callback.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_des_ede3_cfb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BIO_set_callback_arg.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/RSA_meth_get0_app_data.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/o2i_SCT.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OCSP_CRLID_new.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_LOOKUP_get_store.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_set1_curves_list.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OCSP_response_status.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_aes_192_cfb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/PEM_write_bio_PrivateKey_traditional.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/i2d_PKCS12_fp.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/d2i_RSA_PUBKEY.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DSA_bits.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_CRL_verify.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_PKEY_meth_set_keygen.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/i2d_OCSP_REQUEST.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_verify_cb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_COMP_get0_name.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_STORE_CTX_get_get_crl.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EC_GROUP_set_curve.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EC_GROUP_free.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_CTX_set_ssl_version.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_add0_chain_cert.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/ADMISSION_SYNTAX_get0_contentsOfAdmissions.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_aes_256_ocb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EC_GROUP_get_pentanomial_basis.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OPENSSL_instrument_bus.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DH_free.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DSA_meth_get_bn_mod_exp.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_is_bit_set.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_MD_CTX_reset.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_sha512_256.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BIO_append_filename.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_aes_192_cfb8.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_aes_192_ofb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/CMS_RecipientInfo_ktri_cert_cmp.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/CT_POLICY_EVAL_CTX_set_time.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DSA_test_flags.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BIO_set_md.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_BLINDING_invert_ex.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_chacha20_poly1305.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_lebin2bn.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/NETSCAPE_CERT_SEQUENCE_new.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/CRYPTO_zalloc.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DSA_meth_free.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_STORE_set_lookup_crls_cb.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_SIG_INFO_get.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_CTX_get_session_cache_mode.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/i2d_NOTICEREF.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_client_hello_get0_ciphers.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BF_set_key.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/UI_set_method.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_set1_param.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_chain_up_ref.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_aes_128_cfb1.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/EVP_MD_CTX_update_fn.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_stateless.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/PEM_read_CMS.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/CRYPTO_new_ex_data.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_SESSION_dup.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/OCSP_REQUEST_new.3ssl
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/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/BN_dec2bn.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/DES_ecb3_encrypt.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/X509_LOOKUP_meth_set_get_by_alias.3ssl
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/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSL_use_psk_identity_hint.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/SSLv23_client_method.3ssl
/usr/local/Cellar/openssl@1.1/1.1.1g/share/man/man3/d2i_PKCS8_PRIV_KEY_INFO_bio.3ssl
Broken pipe @ io_write -

R version 4.0.1 (2020-06-06) – “See Things Now”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.

Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

install.packages(“Rserve”, “http://rforge.net”, type=“source”)
Installing package into ‘/Users/ywang203/Library/R/3.6/library’
(as ‘lib’ is unspecified)
trying URL ‘http://rforge.net/src/contrib/Rserve_1.8-6.tar.gz’
Content type ‘application/x-gzip’ length 498657 bytes (486 KB)
==================================================
downloaded 486 KB

  • installing source package ‘Rserve’ …
    ** using staged installation
    checking whether to compile the server… yes
    checking whether to compile the client… no
    checking for gcc… /usr/local/Cellar/gcc/8.3.0/bin/gcc-8
    checking whether the C compiler works… no
    configure: error: in /private/var/folders/tm/gsxql1_j2zz23kt4c858p2mj_jz7py/T/RtmpiwyFDj/R.INSTALL485919ad8a64/Rserve': configure: error: C compiler cannot create executables See config.log’ for more details
    ERROR: configuration failed for package ‘Rserve’
  • removing ‘/Users/ywang203/Library/R/3.6/library/Rserve’
  • restoring previous ‘/Users/ywang203/Library/R/3.6/library/Rserve’

The downloaded source packages are in
‘/private/var/folders/tm/gsxql1_j2zz23kt4c858p2mj_jz7py/T/Rtmpg0Jse7/downloaded_packages’
Warning message:
In install.packages(“Rserve”, , “http://rforge.net”, type = “source”) :
installation of package ‘Rserve’ had non-zero exit status

10

One general note: it makes sense to put Logs into a file and attach it to the post that makes reading much easier. If you have a specific part of the log you would want to highlight you could use the formatting.

What version of MacOS are you using. My newly installed R 4.0.1 under macOS Catalina 10.15.5 would reside here:

/Library/Frameworks/R.framework/Versions/4.0/Resources/library

In general my impression is that a compiler is not working. So maybe you would have to reinstall all that again and check some additional discussions from the forum. One definition of madness is to repeat something again and again and expect a different outcome. Unfortunately with IT and especially KNIME and R that is what one would sometimes have to do to be successful.

I have a workflow on the hub that allows for some checks of packages and paths and versions. The results will be stored in a subfolder /result/ beneath the main folder. Also the workflow contains a lot of links about R and KNIME.

If you want you could check the information and maybe share some of it (please note sessionInfo_4.txt will contain some login information you may not want to make public).

image

11

In R or RStudio you could check for compilers which are linked to certain commands

system("which clang")
system("which cc")
system("which gcc")

These will show you the path and version of the compilers (might be the same)

system("gcc --version")
system("cc --version")
system("clang --version")
12

system(“which clang”)
/usr/bin/clang
system(“which cc”)
/usr/bin/cc
system(“which gcc”)
/usr/bin/gcc
system(“gcc --version”)
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
system(“cc --version”)
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
system(“clang --version”)
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

13

My configuration just seems to be about one version ahead and clang one behind. Difficult to tell if this makes any difference, could be worth a try. What I could think of is to try and install it from the local R version (without RStudio) as a package. Or try other suggestions that have been made in the various threads.

system(“gcc --version”)
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.16)
Target: x86_64-apple-darwin19.5.0

14

I posted the issue to Rserve github issue and the owner replied to me at link https://github.com/s-u/Rserve/issues/151
I don’t think i understand his solutions… but I did reinstall gcc via homebrew. I wonder if I need to change R configuration? if so how do i do it?

15

I figured it out!!! so excited :）
I had a makevar configuration in ~/.R/Makevars file set all gcc settings to 8.3.0 while my gcc has already been upgraded to 9.3. so the usr/local/Cellar/gcc directory only has 9.3.0_, not 8.3.0 any more. The Makevars file keeps telling R to compile with 8.3 which pointed to an non-exist directory. I updated the Makevars configuration and I can successfully install the package.

2 Likes
16

Happy to hear that you were able to solve the issue :grinning:.

Best,
Mark

1 Like
17

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