Re: [R] Network issue
Hi Stephen, Thanks again for getting back to me, Ivan Krylov responded also and suggested windows binaries and I must confess I was only familiar with installing from files via the package sources (apart from the conventional install.packages method), so the solution was as simple as installing via the binaries. Thanks again, best wishes, James From: stephen sefick Sent: Wednesday 21 February 2024 12:25 To: James Powell Cc: r-help@r-project.org Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. My suggestion is probably overkill. Sorry about that. I don't know much about windows. Have you tried posit package manager? Maybe that is not blocked? I think windows binaries are installable from there? A workaround, that I don't think I would suggest, might be RSelinium to automate the download process since it seems you have web access? Best of luck! Kindest regards, Stephen Sefick On Wed, Feb 21, 2024, 01:09 James Powell mailto:james.pow...@hse.ie>> wrote: Hi Stephen, I didn’t see this suggested previously, but yes I have made repeated attempts to gain access to CRAN via R but to no avail. Mirroring CRAN is a really good idea, but I’m not sure how to get R to recognise the local file locations when the installation files seek access to CRAN via urls. Thanks again for your help. Regards, James From: stephen sefick mailto:ssef...@gmail.com>> Sent: Wednesday 21 February 2024 00:04 To: James Powell mailto:james.pow...@hse.ie>> Cc: r-help@r-project.org<mailto:r-help@r-project.org> Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. As stated in an earlier email, this might be better directed to your IT? You might think about mirroring CRAN locally, but this would be non-trivial. Stephen Sefick On Tue, Feb 20, 2024, 17:26 James Powell mailto:james.pow...@hse.ie>> wrote: Hi Stephen, Thanks very much for getting back to me. My problem is described below. Any help would be greatly appreciated. Thanks, James Hi, Sorry for bothering you because I know that your time is voluntary, but I would really appreciate some help. I work in a hospital in part of Ireland’s national health service, a service which was struck by a massive cyber attack a couple of years ago. Since then their security has been very tight, and I can’t access the internet through my R or R Studio. To install packages I need to download the files through a browser (Chrome by default) and install them from the files, which is very tedious when you consider the amount of dependencies, but I’m happy to do it. This was working fine until yesterday when I had error messages trying to install some packages. See enclosed “S2” for example. It looks like it is trying to download a file as part of the installation, but of course can’t. If you could help with this I would be very grateful. Other examples are jqr, protolite, curl. I came across a different error message when trying to install openssl, although the issue may be the same. For this package it says Warning in file(name, "wb") : cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied Error in file(name, "wb") : cannot open the connection I have tried going into the archive of these packages and installing older versions, but no luck with those either. I hope you can help. Best wishes, James From: stephen sefick mailto:ssef...@gmail.com>> Sent: Tuesday 20 February 2024 19:43 To: James Powell mailto:james.pow...@hse.ie>> Cc: r-help@r-project.org<mailto:r-help@r-project.org> Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Maybe I missed the rest of the post? You are more likely to get help with your problems if you create a minimal reproducible example. Kindest regards, Stephen Sefick On Tue, Feb 20, 2024, 12:24 James Powell mailto:james.pow...@hse.ie>> wrote: Need information and advice on COVID-19? Go to www.hse.ie/coronavirus<https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fwww.hse.ie%2Fcoronavirus=ceec0a7bd0b1f730294db0447d2a0c1ad2741351> "Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . Seains gurb iad tuairimí pearsanta an úd
Re: [R] Network issue
Hi Stephen, Thanks very much for getting back to me. My problem is described below. Any help would be greatly appreciated. Thanks, James Hi, Sorry for bothering you because I know that your time is voluntary, but I would really appreciate some help. I work in a hospital in part of Ireland’s national health service, a service which was struck by a massive cyber attack a couple of years ago. Since then their security has been very tight, and I can’t access the internet through my R or R Studio. To install packages I need to download the files through a browser (Chrome by default) and install them from the files, which is very tedious when you consider the amount of dependencies, but I’m happy to do it. This was working fine until yesterday when I had error messages trying to install some packages. See enclosed “S2” for example. It looks like it is trying to download a file as part of the installation, but of course can’t. If you could help with this I would be very grateful. Other examples are jqr, protolite, curl. I came across a different error message when trying to install openssl, although the issue may be the same. For this package it says Warning in file(name, "wb") : cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied Error in file(name, "wb") : cannot open the connection I have tried going into the archive of these packages and installing older versions, but no luck with those either. I hope you can help. Best wishes, James From: stephen sefick Sent: Tuesday 20 February 2024 19:43 To: James Powell Cc: r-help@r-project.org Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Maybe I missed the rest of the post? You are more likely to get help with your problems if you create a minimal reproducible example. Kindest regards, Stephen Sefick On Tue, Feb 20, 2024, 12:24 James Powell mailto:james.pow...@hse.ie>> wrote: Need information and advice on COVID-19? Go to www.hse.ie/coronavirus<https://www.hse.ie/coronavirus> "Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach tuairimí FSS iad. Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 300300 nó ar an ríomhphost chuig service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost seo ded' chóras." "Information in this email (including attachments) is confidential. It is intended for receipt and consideration only by the intended recipient. If you are not an addressee or intended recipient, any use, dissemination, distribution, disclosure, publication or copying of information contained in this email is strictly prohibited. Opinions expressed in this email may be personal to the author and are not necessarily the opinions of the HSE. If this email has been received by you in error we would be grateful if you could immediately notify the ICT Service Desk by telephone at +353 818 300300 or by email to service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this e-mail from your system" R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: failed to download mirrors file (cannot open URL 'https://cran.r-project.org/CRAN_mirrors.csv'); using local file 'C:/PROGRA~1/R/R-43~1.1/doc/CRAN_mirrors.csv' Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror In addition: Warning message: In download.file(url, destfile = f, quiet = TRUE) : URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'SSL connect error' > util
Re: [R] Network issue
Hi Ivan, Thanks very much for your response, I'll definitely give that a go. Best wishes, James -Original Message- From: Ivan Krylov Sent: Wednesday 21 February 2024 10:38 To: James Powell Cc: r-help@r-project.org Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. В Wed, 21 Feb 2024 06:09:51 + James Powell пишет: > This was working fine until yesterday when I had error messages trying > to install some packages. See enclosed “S2” for example. It looks like > it is trying to download a file as part of the installation, but of > course can’t. Since you're on Windows and running R-4.3, it should be easier to download and install the binary package, https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fcontrib%2F4.3%2Fs2_1.1.6.zip=40c0076a9193368805cc3e637e09c680a3e72586. Installing this package from source involves downloading a few binaries anyway. You could try unpacking the source package, downloading OpenSSL 1.1.1k binaries from https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fgithub.com%2Frwinlib%2Fopenssl%2Ftree%2Fv1.1.1k=10f7c80b5f4e5dcf0d0f3bd203a067fec29f43a4 into a new subdirectory called windows/ in the package root, just like the https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fgithub.com%2Fr-spatial%2Fs2%2Fblob%2Fmain%2Ftools%2Fwinlibs.R=fd500ed04f0fa1a24bbd7e7e50df6aa7f4bb654c script tries to do during the installation, then installing the resulting directory as if it was a source package. -- Best regards, Ivan Need information and advice on COVID-19? Go to www.hse.ie/coronavirus<https://www.hse.ie/coronavirus> "Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach tuairimí FSS iad. Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 300300 nó ar an ríomhphost chuig service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost seo ded' chóras." "Information in this email (including attachments) is confidential. It is intended for receipt and consideration only by the intended recipient. If you are not an addressee or intended recipient, any use, dissemination, distribution, disclosure, publication or copying of information contained in this email is strictly prohibited. Opinions expressed in this email may be personal to the author and are not necessarily the opinions of the HSE. If this email has been received by you in error we would be grateful if you could immediately notify the ICT Service Desk by telephone at +353 818 300300 or by email to service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this e-mail from your system" __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Network issue
Hi Stephen, I didn’t see this suggested previously, but yes I have made repeated attempts to gain access to CRAN via R but to no avail. Mirroring CRAN is a really good idea, but I’m not sure how to get R to recognise the local file locations when the installation files seek access to CRAN via urls. Thanks again for your help. Regards, James From: stephen sefick Sent: Wednesday 21 February 2024 00:04 To: James Powell Cc: r-help@r-project.org Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. As stated in an earlier email, this might be better directed to your IT? You might think about mirroring CRAN locally, but this would be non-trivial. Stephen Sefick On Tue, Feb 20, 2024, 17:26 James Powell mailto:james.pow...@hse.ie>> wrote: Hi Stephen, Thanks very much for getting back to me. My problem is described below. Any help would be greatly appreciated. Thanks, James Hi, Sorry for bothering you because I know that your time is voluntary, but I would really appreciate some help. I work in a hospital in part of Ireland’s national health service, a service which was struck by a massive cyber attack a couple of years ago. Since then their security has been very tight, and I can’t access the internet through my R or R Studio. To install packages I need to download the files through a browser (Chrome by default) and install them from the files, which is very tedious when you consider the amount of dependencies, but I’m happy to do it. This was working fine until yesterday when I had error messages trying to install some packages. See enclosed “S2” for example. It looks like it is trying to download a file as part of the installation, but of course can’t. If you could help with this I would be very grateful. Other examples are jqr, protolite, curl. I came across a different error message when trying to install openssl, although the issue may be the same. For this package it says Warning in file(name, "wb") : cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied Error in file(name, "wb") : cannot open the connection I have tried going into the archive of these packages and installing older versions, but no luck with those either. I hope you can help. Best wishes, James From: stephen sefick mailto:ssef...@gmail.com>> Sent: Tuesday 20 February 2024 19:43 To: James Powell mailto:james.pow...@hse.ie>> Cc: r-help@r-project.org<mailto:r-help@r-project.org> Subject: Re: [R] Network issue CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Maybe I missed the rest of the post? You are more likely to get help with your problems if you create a minimal reproducible example. Kindest regards, Stephen Sefick On Tue, Feb 20, 2024, 12:24 James Powell mailto:james.pow...@hse.ie>> wrote: Need information and advice on COVID-19? Go to www.hse.ie/coronavirus<https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fwww.hse.ie%2Fcoronavirus=ceec0a7bd0b1f730294db0447d2a0c1ad2741351> "Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach tuairimí FSS iad. Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 300300 nó ar an ríomhphost chuig service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost seo ded' chóras." "Information in this email (including attachments) is confidential. It is intended for receipt and consideration only by the intended recipient. If you are not an addressee or intended recipient, any use, dissemination, distribution, disclosure, publication or copying of information contained in this email is strictly prohibited. Opinions expressed in this email may be personal to the author and are not necessarily the opinions of the HSE. If this email has been received by you in error we would be grateful if you could immediately notify the ICT Service Desk by telephone at +353 818 300300 or by email to service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this e-mail from your system" Need information and advice on COVID-19? Go to www.hse.ie/coronavirus<https://www.hse.ie/coronavirus> __
[R] Network issue
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot open URL
'https://cran.r-project.org/CRAN_mirrors.csv'); using local file
'C:/PROGRA~1/R/R-43~1.1/doc/CRAN_mirrors.csv'
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'SSL connect
error'
> utils:::menuInstallLocal()
Warning in file(name, "wb") :
cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied
Error in file(name, "wb") : cannot open the connection
Warning message:
In install.packages(files[tarballs], .libPaths()[1L], repos = NULL, :
installation of package ‘C:/Users/jpowell/DOWNLO~1/openssl_2.1.1 (1).tar.gz’
had non-zero exit status
> utils:::menuInstallLocal()
* installing *source* package 's2' ...
** package 's2' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include'
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall
-mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include'
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall
-mfpmath=sse -msse2 -mstackrealign -c cpp-compat.cpp -o cpp-compat.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include'
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall
-mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
g+
In file included from ../src/s2/s2cap.h:26,
from ../src/s2/s2convex_hull_query.h:25,
from s2geography/accessors-geog.h:4,
from s2geography.h:4,
from geography.h:7,
from geography-operator.h:7,
from s2-accessors.cpp:2:
../src/s2/encoded_uint_vector.h: In function 'void
s2coding::EncodeUintWithLength(T, int, Encoder*)':
../src/s2/base/logging.h:169:47: warning: comparison of integer expressions of
different signedness: 'size_t' {aka 'long long unsigned int'} and 'int'
[-Wsign-compare]
169 | #define S2_DCHECK_GE(val1, val2) S2_DCHECK_OP(>=, val1, val2)
| ^
../src/s2/base/logging.h:151:22: note: in definition of macro 'S2_DCHECK'
151 | while (false && (condition)) S2NullStream()
| ^
../src/s2/base/logging.h:169:34: note: in expansion of macro 'S2_DCHECK_OP'
169 | #define S2_DCHECK_GE(val1, val2) S2_DCHECK_OP(>=, val1, val2)
| ^~~~
../src/s2/encoded_uint_vector.h:134:3: note: in expansion of macro
'S2_DCHECK_GE'
134 | S2_DCHECK_GE(encoder->avail(), length);
| ^~~~
../src/s2/encoded_uint_vector.h: In instantiation of 'T
s2coding::EncodedUintVector::operator[](int) const [with T = long long
unsigned int]':
../src/s2/encoded_string_vector.h:146:47: required from here
../src/s2/encoded_uint_vector.h:246:25: warning: comparison of integer
expressions of different signedness: 'int' and 'const uint32' {aka 'const
unsigned int'} [-Wsign-compare]
246 | S2_DCHECK(i >= 0 && i < size_);
| ~~^~~
