RobinHankin / gsl

an R wrapper for the Gnu Scientific Library

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compilation warnings #2

Closed RobinHankin closed 1 year ago

RobinHankin commented 5 years ago

clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c multimin.c -o multimin.o
multimin.c:242:10: warning: incompatible pointer types passing 'gsl_multimin_fminimizer *' to parameter of type 'SEXP'
      (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
        PROTECT(gsl_state);
                ^~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:809:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1561:21: note: passing argument to parameter here
SEXP Rf_protect(SEXP);
                    ^
multimin.c:253:10: warning: incompatible pointer types passing 'gsl_multimin_fdfminimizer *' to parameter of type 'SEXP'
      (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
        PROTECT(gsl_state);
                ^~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:809:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1561:21: note: passing argument to parameter here
SEXP Rf_protect(SEXP);
                    ^
multimin.c:286:10: warning: incompatible pointer types passing 'gsl_multimin_fdfminimizer *' to parameter of type 'SEXP'
      (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
        PROTECT(gsl_state);
                ^~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:809:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1561:21: note: passing argument to parameter here
SEXP Rf_protect(SEXP);
                    ^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c poly.c -o poly.o

RobinHankin commented 5 years ago

* checking whether package ‘gsl’ can be installed ... WARNING
Found the following significant warnings:
  multimin.c:242:10: warning: incompatible pointer types passing 'gsl_multimin_fminimizer *' to parameter of type 'SEXP' (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
  multimin.c:253:10: warning: incompatible pointer types passing 'gsl_multimin_fdfminimizer *' to parameter of type 'SEXP' (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
  multimin.c:286:10: warning: incompatible pointer types passing 'gsl_multimin_fdfminimizer *' to parameter of type 'SEXP' (aka 'struct SEXPREC *') [-Wincompatible-pointer-types]
See ‘/Users/rhankin/rstudio/gsl.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK

[snip]

* checking examples ...sh: line 1: 68209 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'gsl-Ex.Rout' 2>&1 < gsl-Ex.R
 ERROR
Running examples in ‘gsl-Ex.R’ failed
The error most likely occurred in:

> ### Name: multimin
> ### Title: Function minimization
> ### Aliases: Multimin multimin multimin.init multimin.iterate
> ###   multimin.restart multimin.fminimizer.size
> ### Keywords: array
> 
> ### ** Examples
> 
> # The Rosenbrock function:
> x0 <- c(-1.2, 1)
> f <- function(x) (1 - x[1])^2 + 100 * (x[2] - x[1]^2)^2
> df <- function(x) c(-2*(1 - x[1]) + 100 * 2 * (x[2] - x[1]^2) * (-2*x[1]),
+                     100 * 2 * (x[2] - x[1]^2))
> 
> # The simple way to call multimin.
> state <- multimin(x0, f, df)

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: multimin.iterate(state)
 2: multimin(x0, f, df)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘gslpaper.Rnw’ ... OK

ddalthorp commented 5 years ago

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

RobinHankin commented 5 years ago

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp notifications@github.com wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/RobinHankin/gsl/issues/2?email_source=notifications&email_token=ADFFZURD44JSDYQMSRMFKLLP3FUW5A5CNFSM4G3UA2DKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYAHP5Q#issuecomment-503347190, or mute the thread https://github.com/notifications/unsubscribe-auth/ADFFZURXY6LZVB44LUHCYVTP3FUW5ANCNFSM4G3UA2DA .

ddalthorp commented 5 years ago

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

include <gsl/gsl_sf_airy.h>

compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin notifications@github.com wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp notifications@github.com wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/RobinHankin/gsl/issues/2?email_source=notifications&email_token=ADFFZURD44JSDYQMSRMFKLLP3FUW5A5CNFSM4G3UA2DKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYAHP5Q#issuecomment-503347190 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ADFFZURXY6LZVB44LUHCYVTP3FUW5ANCNFSM4G3UA2DA

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-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

RobinHankin commented 5 years ago

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp notifications@github.com wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin notifications@github.com wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp notifications@github.com wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/RobinHankin/gsl/issues/2?email_source=notifications&email_token=ADFFZUWD4UJJULLYH3OLQW3P3F42VA5CNFSM4G3UA2DKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYAKWQY#issuecomment-503360323, or mute the thread https://github.com/notifications/unsubscribe-auth/ADFFZUXJ3GHCG32A2CMIYOLP3F42VANCNFSM4G3UA2DA .

ddalthorp commented 5 years ago

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin notifications@github.com wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp notifications@github.com wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin notifications@github.com wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp notifications@github.com wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/RobinHankin/gsl/issues/2?email_source=notifications&email_token=ADFFZUWD4UJJULLYH3OLQW3P3F42VA5CNFSM4G3UA2DKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYAKWQY#issuecomment-503360323 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ADFFZUXJ3GHCG32A2CMIYOLP3F42VANCNFSM4G3UA2DA

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-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

RobinHankin commented 5 years ago

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp notifications@github.com wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin notifications@github.com wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp notifications@github.com wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin <notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp <notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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ddalthorp commented 5 years ago

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin notifications@github.com wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp notifications@github.com wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin notifications@github.com wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp notifications@github.com wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

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RobinHankin commented 5 years ago

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp notifications@github.com wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin notifications@github.com wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp notifications@github.com wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin <notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp <notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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ddalthorp commented 5 years ago

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin notifications@github.com wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp notifications@github.com wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin notifications@github.com wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp notifications@github.com wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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RobinHankin commented 5 years ago

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin notifications@github.com wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp notifications@github.com wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin <notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp notifications@github.com wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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ddalthorp commented 5 years ago

I understand your question. I don't know the answer.

What I do know is that I installed the gsl package (Windows binary) from CRAN and have been using it for several years. I don't think I ever installed the GSL library, and if I did, I do not know where it is on my machine or how to find out which version it is; or whether the gsl package is using that library or uses a version that was bundled into the package at CRAN.

I also know that Travis can no longer build my GenEst package using project files that worked fine for me not long ago. The error message it gives references problems in the gsl package, as I quoted before. I'm pretty sure that Travis is not looking for GSL on my machine and that my code does not include any references to GSL or its functions beyond listing gsl as a dependency and then calling one or two of the gsl functions.

On Wed, Jun 19, 2019 at 5:56 PM Robin Hankin notifications@github.com wrote:

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin notifications@github.com wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp notifications@github.com wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin < notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp < notifications@github.com> wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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RobinHankin commented 5 years ago

hi there, the warnings are caused by using too old version of GSL. You will have to upgrade in order to compile. I'm pretty sure that Travis uses an old version of GSL which is causing the problems. I am not sure what the proper .travis.yml lines to load GSL-2.5 would look like, sorry. I also need to update the configure.ac script to reflect this, clearly a bug in gsl.

best wishes

Robin

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 2:05 PM ddalthorp notifications@github.com wrote:

I understand your question. I don't know the answer.

What I do know is that I installed the gsl package (Windows binary) from CRAN and have been using it for several years. I don't think I ever installed the GSL library, and if I did, I do not know where it is on my machine or how to find out which version it is; or whether the gsl package is using that library or uses a version that was bundled into the package at CRAN.

I also know that Travis can no longer build my GenEst package using project files that worked fine for me not long ago. The error message it gives references problems in the gsl package, as I quoted before. I'm pretty sure that Travis is not looking for GSL on my machine and that my code does not include any references to GSL or its functions beyond listing gsl as a dependency and then calling one or two of the gsl functions.

On Wed, Jun 19, 2019 at 5:56 PM Robin Hankin notifications@github.com wrote:

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin <notifications@github.com

wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp notifications@github.com wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin < notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp < notifications@github.com> wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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RobinHankin commented 5 years ago

hello again, I've updated the gsl repo and included some new lines in the .travis.yml file ....and now get the same errors as you reported. I am not sure what to do about this other than wait for

sudo apt-get install libgsl0-dev to install sufficiently a new version of GSL.

best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:31 PM robin hankin hankin.robin@gmail.com wrote:

hi there, the warnings are caused by using too old version of GSL. You will have to upgrade in order to compile. I'm pretty sure that Travis uses an old version of GSL which is causing the problems. I am not sure what the proper .travis.yml lines to load GSL-2.5 would look like, sorry. I also need to update the configure.ac script to reflect this, clearly a bug in gsl.

best wishes

Robin

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 2:05 PM ddalthorp notifications@github.com wrote:

I understand your question. I don't know the answer.

What I do know is that I installed the gsl package (Windows binary) from CRAN and have been using it for several years. I don't think I ever installed the GSL library, and if I did, I do not know where it is on my machine or how to find out which version it is; or whether the gsl package is using that library or uses a version that was bundled into the package at CRAN.

I also know that Travis can no longer build my GenEst package using project files that worked fine for me not long ago. The error message it gives references problems in the gsl package, as I quoted before. I'm pretty sure that Travis is not looking for GSL on my machine and that my code does not include any references to GSL or its functions beyond listing gsl as a dependency and then calling one or two of the gsl functions.

On Wed, Jun 19, 2019 at 5:56 PM Robin Hankin notifications@github.com wrote:

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin < notifications@github.com> wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp <notifications@github.com

wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin < notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp < notifications@github.com> wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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RobinHankin commented 5 years ago

hello again, gsl now clean under travis (not sure why I used libgsl0-dev rather than libgsl-dev).

Best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Fri, Jun 21, 2019 at 11:41 AM robin hankin hankin.robin@gmail.com wrote:

hello again, I've updated the gsl repo and included some new lines in the .travis.yml file ....and now get the same errors as you reported. I am not sure what to do about this other than wait for

sudo apt-get install libgsl0-dev to install sufficiently a new version of GSL.

best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:31 PM robin hankin hankin.robin@gmail.com wrote:

hi there, the warnings are caused by using too old version of GSL. You will have to upgrade in order to compile. I'm pretty sure that Travis uses an old version of GSL which is causing the problems. I am not sure what the proper .travis.yml lines to load GSL-2.5 would look like, sorry. I also need to update the configure.ac script to reflect this, clearly a bug in gsl.

best wishes

Robin

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 2:05 PM ddalthorp notifications@github.com wrote:

I understand your question. I don't know the answer.

What I do know is that I installed the gsl package (Windows binary) from CRAN and have been using it for several years. I don't think I ever installed the GSL library, and if I did, I do not know where it is on my machine or how to find out which version it is; or whether the gsl package is using that library or uses a version that was bundled into the package at CRAN.

I also know that Travis can no longer build my GenEst package using project files that worked fine for me not long ago. The error message it gives references problems in the gsl package, as I quoted before. I'm pretty sure that Travis is not looking for GSL on my machine and that my code does not include any references to GSL or its functions beyond listing gsl as a dependency and then calling one or two of the gsl functions.

On Wed, Jun 19, 2019 at 5:56 PM Robin Hankin notifications@github.com wrote:

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin < notifications@github.com> wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp < notifications@github.com> wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin < notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp < notifications@github.com> wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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ddalthorp commented 5 years ago

fantastic! nice bug hunting.

On Sun, Jun 23, 2019 at 3:43 PM Robin Hankin notifications@github.com wrote:

hello again, gsl now clean under travis (not sure why I used libgsl0-dev rather than libgsl-dev).

Best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Fri, Jun 21, 2019 at 11:41 AM robin hankin hankin.robin@gmail.com wrote:

hello again, I've updated the gsl repo and included some new lines in the .travis.yml file ....and now get the same errors as you reported. I am not sure what to do about this other than wait for

sudo apt-get install libgsl0-dev to install sufficiently a new version of GSL.

best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:31 PM robin hankin hankin.robin@gmail.com wrote:

hi there, the warnings are caused by using too old version of GSL. You will have to upgrade in order to compile. I'm pretty sure that Travis uses an old version of GSL which is causing the problems. I am not sure what the proper .travis.yml lines to load GSL-2.5 would look like, sorry. I also need to update the configure.ac script to reflect this, clearly a bug in gsl.

best wishes

Robin

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 2:05 PM ddalthorp notifications@github.com wrote:

I understand your question. I don't know the answer.

What I do know is that I installed the gsl package (Windows binary) from CRAN and have been using it for several years. I don't think I ever installed the GSL library, and if I did, I do not know where it is on my machine or how to find out which version it is; or whether the gsl package is using that library or uses a version that was bundled into the package at CRAN.

I also know that Travis can no longer build my GenEst package using project files that worked fine for me not long ago. The error message it gives references problems in the gsl package, as I quoted before. I'm pretty sure that Travis is not looking for GSL on my machine and that my code does not include any references to GSL or its functions beyond listing gsl as a dependency and then calling one or two of the gsl functions.

On Wed, Jun 19, 2019 at 5:56 PM Robin Hankin <notifications@github.com

wrote:

No, I mean the GSL library as in https://www.gnu.org/software/gsl/ hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 9:42 AM ddalthorp notifications@github.com wrote:

not sure...or even how to tell. I'm using whatever CRAN gives me.

On Wed, Jun 19, 2019 at 1:34 PM Robin Hankin < notifications@github.com> wrote:

I meant the library, not the package. the most recent GSL is 2.5 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Thu, Jun 20, 2019 at 3:20 AM ddalthorp < notifications@github.com> wrote:

I have gsl 2.1.6 on my machine. I presume Travis is using the most up-to-date version at CRAN.

On Wed, Jun 19, 2019 at 2:38 AM Robin Hankin < notifications@github.com

wrote:

what version of GSL are you using? some of the functions changed from version 1 to 2 hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 1:48 PM ddalthorp < notifications@github.com> wrote:

I use rcpp in several packages (e.g., GenEst and cbinom on CRAN and eoa at USGS) and am having no trouble either with rtools or building those packages. Is that akin to what you had in mind?

Also, I am able to build all the other GenEst dependencies (corpus, DT, tools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival) without trouble.

For gsl in Travis, I get the following warnings and errors for gsl:

ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’

removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status

On Tue, Jun 18, 2019 at 6:06 PM Robin Hankin < notifications@github.com

wrote:

Im not really sure what to recommend here, the package is clean on CRAN (except some macosx issues). I tried to build gsl on travis, which gave me a failing build for some reason which I didn't understand. Can you compile a hello world C program on your platform? That would be the first step, let me know how it goes.

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 12:30 PM ddalthorp < notifications@github.com

wrote:

I'm having the same issue on my desktop, running R 3.5.2 in Rgui.exe for Windows.

install.packages("gsl",repos = getOption("repos"), repo=NULL, type="source") Installing package into ‘C:/Users/ddalthorp/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL ' http://cran.at.r-project.org/src/contrib/gsl_2.1-6.tar.gz' Content type 'application/x-gzip' length 189794 bytes (185 KB) downloaded 185 KB

installing source package 'gsl' ... ** package 'gsl' successfully unpacked and MD5 sums checked

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

On Tue, Jun 18, 2019 at 5:06 PM Robin Hankin < notifications@github.com

wrote:

hmm, it looks as though the GSL library is not installed properly, if the package can't find airy then the library is not found. I've had similar problems with travis for some of my other packages without any resolution. If I add travis checking to gsl that might help?

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 19, 2019 at 11:21 AM ddalthorp < notifications@github.com

wrote:

I've been using gsl as a dependency for years in two or three of my packages, but just recently I have been unable to install it from source. This is causing my Travis CI checks to fail and has led to a bottleneck in development. Do you have any fixes or suggestions?

Error message is:

WARNING: this package has a configure script It probably needs manual configuration

** libs

*** arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA1/R/R-351.2/include" -DNDEBUG -I/include -O3 -Wall -std=gnu99 -mtune=generic -c airy.c -o airy.o airy.c:1:29: fatal error: gsl/gsl_sf_airy.h: No such file or directory

include <gsl/gsl_sf_airy.h>

^ compilation terminated. make: *** [C:/PROGRA1/R/R-351.2/etc/i386/Makeconf:208: airy.o] Error 1 ERROR: compilation failed for package 'gsl'

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ddalthorp commented 5 years ago

still getting errors at Travis (but different from earlier errors):

installing source package ‘gsl’ ... ... gcc -std=gnu99 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I/usr/include -I. -I/home/travis/R-bin/include -fpic -g -O2 -c ellint.c -o ellint.o ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result); ^ make: *** [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’
removing ‘/home/travis/R/Library/gsl’ Error in i.p(...) : (converted from warning) installation of package ‘gsl’ had non-zero exit status Calls: ... with_rprofile_user -> with_envvar -> force -> force -> i.p Execution halted

RobinHankin commented 5 years ago

I'm still figuring out how to use Travis, in particular I am not sure if I can see other users' files. What is in your .travis.yml file. The errors above are from older versions of GSL, so one has to have the latest version installed.

ddalthorp commented 5 years ago

Ah ha! Therein lies an error, I believe: packages:

libgsl0-dbg
libgsl0-dev
libgsl0ldbl What should I be using instead?

On Tue, Jun 25, 2019 at 1:12 PM Robin Hankin notifications@github.com wrote:

I'm still figuring out how to use Travis, in particular I am not sure if I can see other users' files. What is in your .travis.yml file. The errors above are from older versions of GSL, so one has to have the latest version installed.

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RobinHankin commented 5 years ago

Mine is:

gsl % cat .travis.yml

R for travis: see documentation at

https://docs.travis-ci.com/user/languages/r

before_install:

- gem install rake

- sudo apt-get install libgsl-dev

- sudo apt-get install make cmake gcc git libcurl4-openssl-dev

language: R

cache: packages

gsl %

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 26, 2019 at 8:43 AM ddalthorp notifications@github.com wrote:

Ah ha! Therein lies an error, I believe: packages:

libgsl0-dbg

libgsl0-dev

libgsl0ldbl What should I be using instead?

On Tue, Jun 25, 2019 at 1:12 PM Robin Hankin notifications@github.com wrote:

I'm still figuring out how to use Travis, in particular I am not sure if I can see other users' files. What is in your .travis.yml file. The errors above are from older versions of GSL, so one has to have the latest version installed.

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ddalthorp commented 5 years ago

I changed libgsl0-dbg and libgsl0-dev to libgsl-dbg and libgsl-dev and eliminated libgsl0ldbl. Everything appears to work as intended, both at Travis and locally on my machine.

Thanks for all the help and for the great package!

On Tue, Jun 25, 2019 at 1:49 PM Robin Hankin notifications@github.com wrote:

Mine is:

gsl % cat .travis.yml

R for travis: see documentation at

https://docs.travis-ci.com/user/languages/r

before_install:

gem install rake

sudo apt-get install libgsl-dev

sudo apt-get install make cmake gcc git libcurl4-openssl-dev

language: R

cache: packages

gsl %

hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Wed, Jun 26, 2019 at 8:43 AM ddalthorp notifications@github.com wrote:

Ah ha! Therein lies an error, I believe: packages:

libgsl0-dbg

libgsl0-dev

libgsl0ldbl What should I be using instead?

On Tue, Jun 25, 2019 at 1:12 PM Robin Hankin notifications@github.com wrote:

I'm still figuring out how to use Travis, in particular I am not sure if I can see other users' files. What is in your .travis.yml file. The errors above are from older versions of GSL, so one has to have the latest version installed.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

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, or mute the thread <

https://github.com/notifications/unsubscribe-auth/AHFSXP5YAHJ5CC2A77EXL4DP4J32BANCNFSM4G3UA2DA

.

-- Dan Dalthorp, PhD USGS Forest and Rangeland Ecosystem Science Center Forest Sciences Lab, Rm 311 3200 SW Jefferson Way Corvallis, OR 97331 ph: 541-750-0953 ddalthorp@usgs.gov

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dengel92 commented 2 years ago

Hi, I am trying to update my gsl R package to 2.1.7, but I am continuously getting the following error:

* installing *source* package 'gsl' ...
OE> ** package 'gsl' successfully unpacked and MD5 sums checked
OE> staged installation is only possible with locking
OE> ** using non-staged installation
OE> 
OE>    **********************************************
OE>    WARNING: this package has a configure script
OE>          It probably needs manual configuration
OE>    **********************************************
OE> 
OE> 
OE> ** libs
OE> 
OE> *** arch - i386
OE> "C:/rtools40/mingw32/bin/"gcc  -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I/include         -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -Wall -pedantic -fdiagnostics-color=always -c airy.c -o airy.o
OE> airy.c:1:10:fatal error: sl_sf_airy.h: No such file or directory
OE>  #include <gsl/gsl_sf_airy.h>
OE>           ^~~~~~~~~~~~~~~~~~~
OE> compilation terminated.
OE> make: *** [C:/PROGRA~1/R/R-40~1.2/etc/i386/Makeconf:222: airy.o] Error 1
OE> ERROR: compilation failed for package 'gsl'
OE> * removing 'C:/Users/denge/AppData/Local/Temp/RtmpKC5LFE/pkg-lib4d987523766/gsl'

I have tried all of the following:

Making sure R or Rstudio is running as administrator
Updating Rtools
installing pak package and using it to try to install /update the package. Every time I try, I keep getting the same error. More specifically it mentions an airy.h file that can't be found. I need to update this package to install another package that is dependent on it.

Thank you for your help!

ddalthorp commented 2 years ago

try installing precompiled rather than installing from source

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Tuesday, November 2nd, 2021 at 9:13 AM, dengel92 @.***> wrote:

Hi, I am trying to update my gsl R package to 2.1.7, but I am continuously getting the following error:

installing source package 'gsl' ... OE> package 'gsl' successfully unpacked and MD5 sums checked OE> staged installation is only possible with locking OE> using non-staged installation OE> OE> ** OE> WARNING: this package has a configure script OE> It probably needs manual configuration OE> ** OE> OE> OE> libs OE> OE> ** arch - i386 OE> "C:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I/include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -Wall -pedantic -fdiagnostics-color=always -c airy.c -o airy.o OE> airy.c:1:10:fatal error: sl_sf_airy.h: No such file or directory OE> #include <gsl/gsl_sf_airy.h> OE> ^~~~~~~ OE> compilation terminated. OE> make: [C:/PROGRA~1/R/R-40~1.2/etc/i386/Makeconf:222: airy.o] Error 1 OE> ERROR: compilation failed for package 'gsl' OE> * removing 'C:/Users/denge/AppData/Local/Temp/RtmpKC5LFE/pkg-lib4d987523766/gsl'

I have tried all of the following:

Making sure R or Rstudio is running as administrator

Updating Rtools

installing pak package and using it to try to install /update the package. Every time I try, I keep getting the same error. More specifically it mentions an airy.h file that can't be found. I need to update this package to install another package that is dependent on it.

Thank you for your help!

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