installation of package ‘RCurl’ had non-zero exit status

[Chrischen]

R-3.6.0-win
RStudio-1.2.5042
Rtools35
Computer:Windows 10 64 bit
I have not processed the data for a while, previously the installment of "SARtools" works and i used it work for several times. Recently, i have new data to process, but find the SARtools does not work, so i tried to install it again.
Here is the command i run:
install.packages("devtools")
library(devtools)
install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)
Then i got warning:
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.0/etc/x64/Makeconf:208: base64.o] Error 1
ERROR: compilation failed for package 'RCurl'

• removing 'C:/Users/97142/Documents/R/win-library/3.6/RCurl'
  Warning in install.packages :
  installation of package ‘RCurl’ had non-zero exit status
  , anyone can provide some hint is appreciated

[Chrischen]

Any information will be apprecaited

[andresrcs]

@Chrischen

install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)

Can you post all the message output you get when you run this command?

[Chrischen]

install.packages("remotes")
Installing package into ‘C:/Users/97142/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Content type 'application/zip' length 358520 bytes (350 KB)
downloaded 350 KB

package ‘remotes’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\97142\AppData\Local\Temp\RtmpwBhEqz\downloaded_packages
remotes::install_github("PF2-pasteur-fr/SARTools")
Downloading GitHub repo PF2-pasteur-fr/SARTools@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RCurl (1.98-1.1 -> 1.98-1.2) [CRAN]
5: isoband (0.2.0 -> 0.2.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
1
RCurl (1.98-1.1 -> 1.98-1.2) [CRAN]
isoband (0.2.0 -> 0.2.1 ) [CRAN]
Installing 2 packages: RCurl, isoband
Installing packages into ‘C:/Users/97142/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

There are binary versions available but the source versions are
later:
binary source needs_compilation
RCurl 1.98-1.1 1.98-1.2 TRUE
isoband 0.2.0 0.2.1 TRUE

installing the source packages ‘RCurl’, ‘isoband’

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.98-1.2.tar.gz'
Content type 'application/x-gzip' length 699583 bytes (683 KB)
downloaded 683 KB

trying URL 'https://cran.rstudio.com/src/contrib/isoband_0.2.1.tar.gz'
Content type 'application/x-gzip' length 2293333 bytes (2.2 MB)
downloaded 2.2 MB

• installing source package 'RCurl' ...
  ** package 'RCurl' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  C:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG -I/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -DHAVE_CURLOPT_WRITEDATA=1 -DCURL_STATICLIB -O2 -Wall -std=gnu99 -mtune=core2 -c base64.c -o base64.o
  In file included from base64.c:1:0:
  Rcurl.h:4:23: fatal error: curl/curl.h: No such file or directory
  #include <curl/curl.h>
  ^
  compilation terminated.
  make: *** [C:/PROGRA~1/R/R-36~1.3/etc/x64/Makeconf:208: base64.o] Error 1
  ERROR: compilation failed for package 'RCurl'
• removing 'C:/Users/97142/Documents/R/win-library/3.6/RCurl'
• restoring previous 'C:/Users/97142/Documents/R/win-library/3.6/RCurl'
  Error: Failed to install 'SARTools' from GitHub:
  (converted from warning) installation of package ‘RCurl’ had non-zero exit status

R3.6.3 For windows
If the information is not good enough, please tell me

[Chrischen]

thanks for your reply!
here is the command and message:
remotes::install_github("PF2-pasteur-fr/SARTools")
Downloading GitHub repo PF2-pasteur-fr/SARTools@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RCurl (1.98-1.1 -> 1.98-1.2) [CRAN]
5: isoband (0.2.0 -> 0.2.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
1
RCurl (1.98-1.1 -> 1.98-1.2) [CRAN]
isoband (0.2.0 -> 0.2.1 ) [CRAN]
Installing 2 packages: RCurl, isoband
Installing packages into ‘C:/Users/97142/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

There are binary versions available but the source versions are
later:
binary source needs_compilation
RCurl 1.98-1.1 1.98-1.2 TRUE
isoband 0.2.0 0.2.1 TRUE

installing the source packages ‘RCurl’, ‘isoband’

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.98-1.2.tar.gz'
Content type 'application/x-gzip' length 699583 bytes (683 KB)
downloaded 683 KB

trying URL 'https://cran.rstudio.com/src/contrib/isoband_0.2.1.tar.gz'
Content type 'application/x-gzip' length 2293333 bytes (2.2 MB)
downloaded 2.2 MB

• installing source package 'RCurl' ...
  ** package 'RCurl' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  C:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-36~1.3/include" -DNDEBUG -I/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -DHAVE_CURLOPT_WRITEDATA=1 -DCURL_STATICLIB -O2 -Wall -std=gnu99 -mtune=core2 -c base64.c -o base64.o
  In file included from base64.c:1:0:
  Rcurl.h:4:23: fatal error: curl/curl.h: No such file or directory
  #include <curl/curl.h>
  ^
  compilation terminated.
  make: *** [C:/PROGRA~1/R/R-36~1.3/etc/x64/Makeconf:208: base64.o] Error 1
  ERROR: compilation failed for package 'RCurl'
• removing 'C:/Users/97142/Documents/R/win-library/3.6/RCurl'
• restoring previous 'C:/Users/97142/Documents/R/win-library/3.6/RCurl'
  Error: Failed to install 'SARTools' from GitHub:
  (converted from warning) installation of package ‘RCurl’ had non-zero exit status

Looking forward to your reply!

[andresrcs]

It seemes to be an issue with the source code of RCurl try updating only isoband for now and see if installation of SARTools can continue that way. If it fails, then you are going to have to wait some days until a binary version of RCurl (that doesn't require compilation) is available for Windows.

[Chrischen]

Thank you so much for your reply!
I have tired several time then, try to run similar command

remotes::install_github("PF2-pastrue-fr/SARTools")

similar warning
Error: Failed to install 'SARTools' from GitHub:
(converted from warning) installation of package ‘RCurl’ had non-zero exit status
install.packages("SARTools")
Installing package into ‘C:/Users/97142/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘SARTools’ is not available (for R version 3.6.3)
it seems that Rcurl is essential for the running of installment of SARTools.

I appreciate for your help!

[andresrcs]

@Chrischen

similar warning
Error: Failed to install 'SARTools' from GitHub:
(converted from warning) installation of package ‘RCurl’ had non-zero exit status

It seems to me that you are still trying to install RCurl, my advice is to select option 5 when asked and see if the installation process can continue.

@Chrischen

5: isoband (0.2.0 -> 0.2.1 ) [CRAN]

[Chrischen]

Thanks for the detail

[Chrischen]

@Chrischen

remotes::install_github("PF2-pasteur-fr/SARTools")
Downloading GitHub repo PF2-pasteur-fr/SARTools@master

Thanks for so detailed information, yes, it works now,
+.gg ggplot2
----------------------------------------------
Welcome to SARTools version 1.7.2.
R template scripts are available on GitHub.
----------------------------------------------
But when i continue to do analysis, new problem come up:

majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
Matrix of SERE statistics:
WT-1 WT-2 WT-3 atxr56-1 atxr56-2 atxr56-3
WT-1 0.000 9.845 11.136 7.627 9.962 10.110
WT-2 9.845 0.000 5.398 7.643 5.128 7.052
WT-3 11.136 5.398 0.000 6.974 5.909 7.598
atxr56-1 7.627 7.643 6.974 0.000 7.923 7.469
atxr56-2 9.962 5.128 5.909 7.923 0.000 3.602
atxr56-3 10.110 7.052 7.598 7.469 3.602 0.000
Warning messages:
1: expand_scale() is deprecated; use expansion() instead.
2: expand_scale() is deprecated; use expansion() instead.
3: expand_scale() is deprecated; use expansion() instead.
Looks for the new SARTools, some thing changes, i can not use previous command, could you please tell me what change should i make?

[andresrcs]

This is a different question, please ask it on a new topic providing a proper REPRoducible EXample (reprex) illustrating your issue.

[Chrischen]

Thanks, i tried to continue and it works, looks not a big deal!
Thanks a lot for your help! Hope everything is doing alright at your end!