Open btojenniferborder opened 8 months ago
urisohn
commented
8 months ago Can you check whether those URLs work on your browser? http://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip
The server may be blocking your IP. So, this may be a useful first thing to rule out/in/
btojenniferborder
commented
8 months ago Ah yes, it says it's blocked. Any idea how I get round this?
On Tue, 23 Jan 2024 at 11:15, Uri Simonsohn @.***> wrote:
Can you check whether those URLs work on your browser? http://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip
The server may be blocking your IP. So, this may be a useful first thing to rule out/in/
— Reply to this email directly, view it on GitHub https://github.com/CredibilityLab/groundhog/issues/112#issuecomment-1905824124, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPNFIJW7T62INMZJBIPDPLYP6LU5AVCNFSM6AAAAABCGY76GSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBVHAZDIMJSGQ . You are receiving this because you authored the thread.Message ID: @.***>
--
Dr Jennifer Border (*née* Taylor) Senior Research Ecologist
British Trust for Ornithology, The Nunnery, Thetford, Norfolk IP24 2PU Tel: +44 (0) 1842 750050 Fax: +44 (0) 1842 750030 Email: jennifer.border @bto.org @.***>
Registered Charity Number 216652 (England & Wales), SC039193 (Scotland). Company Limited by Guarantee Number 357284 (England and Wales).
urisohn
commented
8 months ago Option 1. use option force.source=TRUE, it will download from CRAN, but be slower Option 2. turn on a VPN if you have one.
Will look into why the GRAN server may be blocking your IP
urisohn
commented
8 months ago (i am revising groundhog and will include a more elegant error message when it fails to connect)
btojenniferborder
commented
8 months ago Ah it still failed for lme4 and glmmTMB:
Batch 2 of 2 has 1 packages. It is: lme4_1.1-29 As of 11:52 this batch is expected to finish installing by 11:53 (but these are noisy estimates).
You can keep trak of installation progress and expected completion time opening this real-time updated text file: C:\Users\jennifer.border\Documents\R_groundhog\groundhog_library\install_progress.txt
trying URL ' https://cran.rstudio.com//src/contrib/Archive/lme4/lme4_1.1-29.tar.gz' Content type 'application/x-gzip' length 3306026 bytes (3.2 MB) downloaded 3.2 MB
| -I"C:/Users/jennifer.border/Documents/R/win-library/4.2/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c external.cpp -o external.o In file included from predModule.h:13, from external.cpp:8: lme4CholmodDecomposition.h:20:72: error: expected template-name before '<' token 20 | class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> { |
|---|
^
lme4CholmodDecomposition.h:20:72: error: expected '{' before '<' token
In file included from predModule.h:13,
from external.cpp:8:
lme4CholmodDecomposition.h: In function 'SEXPREC
lme4::Eigen_cholmod_wrap(const
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix~~~~~
lme4CholmodDecomposition.h:78:13: error: 'f' was not declared in this scope
78 | if (f->minor < f->n)
| ^
lme4CholmodDecomposition.h:82:36: error: 'f' was not declared in this scope
82 | ::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" :
"dCHMsimpl"));
| ^
In file included from external.cpp:8:
predModule.h: At global scope:
predModule.h:40:23: error: field 'd_L' has incomplete type
'lme4::merPredD::ChmDecomp' {aka
'lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
40 | ChmDecomp d_L;
| ^~~
In file included from predModule.h:13,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of
'lme4::merPredD::ChmDecomp' {aka 'class
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
20 | class lme4CholmodDecomposition : public
Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
| ^~~~~~~~
external.cpp: In function 'SEXPREC glmerAGQ(SEXP, SEXP, SEXP, SEXP, SEXP,
SEXP, SEXP)':
external.cpp:437:18: error: invalid use of incomplete type 'const
ChmDecomp' {aka 'const class
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
437 | if (pp->L().factor()->nzmax != q)
| ~^~
In file included from predModule.h:13,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of
'lme4::merPredD::ChmDecomp' {aka 'class
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
20 | class lme4CholmodDecomposition : public
Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
| ^~~~~~~~
external.cpp:439:49: error: invalid use of incomplete type 'const
ChmDecomp' {aka 'const class
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
439 | const Ar1 sd(MAr1((double)pp->L().factor()->x,
q).inverse());
| ~^~
In file included from predModule.h:13,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of
'lme4::merPredD::ChmDecomp' {aka 'class
lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >'}
20 | class lme4CholmodDecomposition : public
Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
| ^~~~~~~~
make: *** [C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf:259: external.o] Error 1
ERROR: compilation failed for package 'lme4'
The following package(s) from this batch failed to install: 'lme4_1.1-29'
Possible solutions:
1) First, simply try again, the error may be a fluke.
2) Inspect console log, you could be missing non-CRAN dependencies
(e.g., RTools for Windows, XQuartz for Mac, libssl for Ubuntu),
or have a connection problem, or another compatibility problem.
3) If the error indicates that a dependency is missing, re-run the
groundhog.library() call with option force.install=TRUE
4) If the package that failed is a dependency for a package you want,
you may install another version of that failed dependency directly
with a groundhog.library() call, just for that failing pkg, for a
different date. Then re-run this groundhog.library() call adding the
ignore.deps argument, to allowing the version mismatch for that pkg.
Use toc(<pkg>) to find out version release dates of 'pkg'.
5) Similar to (4), use toc(
-- Installation Failed --Warning message: In utils::install.packages(snowball.k_source$source_url, repos = NULL, : installation of package ‘C:/Users/JENNIF~1.BOR/AppData/Local/Temp/RtmpETYsVr/downloaded_packages/lme4_1.1-29.tar.gz’ had non-zero exit status
On Tue, 23 Jan 2024 at 11:21, Uri Simonsohn @.***> wrote:
(i am revising groundhog and will include a more elegant error message when it fails to connect)
— Reply to this email directly, view it on GitHub https://github.com/CredibilityLab/groundhog/issues/112#issuecomment-1905832962, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPNFIN43HZHTH7QJKVWG33YP6MKRAVCNFSM6AAAAABCGY76GSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBVHAZTEOJWGI . You are receiving this because you authored the thread.Message ID: @.***>
--
Dr Jennifer Border (*née* Taylor) Senior Research Ecologist
British Trust for Ornithology, The Nunnery, Thetford, Norfolk IP24 2PU Tel: +44 (0) 1842 750050 Fax: +44 (0) 1842 750030 Email: jennifer.border @bto.org @.***>
Registered Charity Number 216652 (England & Wales), SC039193 (Scotland). Company Limited by Guarantee Number 357284 (England and Wales).
urisohn
commented
8 months ago Based on the console output the failure is unrelated to groundhog, just a problem compiling it in your computer (most likelyi it would fail not with groundhog (i.e., installing with install.packages(), from source) too). If you don't have a VPN, you could use your phone as a hotspot and install from there (it will be a few MB of traffic only); i haven't yet looked at why the IP may be blocked by the GRAN server
urisohn
commented
8 months ago i got in contact with support for the hosting company that hosts the GRAN database, they indicate that they do not blog IP addresses; one possibility they suggested is that you have a firewall that is preventing access to it. Does that sound plausible?
btojenniferborder
commented
8 months ago H, Thanks for checking. Yes that's definitely possible. I was accessing through my work VPN and there are definitely various different security measures in place on their computer systems. It's not an easy one to get round though as they won't take down the security measures just for me and I can't access through my home laptop as I don't have enough room to store all the data files I use on there.
On Fri, 26 Jan 2024 at 08:30, Uri Simonsohn @.***> wrote:
i got in contact with support for the hosting company that hosts the GRAN database, they indicate that they do not blog IP addresses; one possibility they suggested is that you have a firewall that is preventing access to it. Does that sound plausible?
— Reply to this email directly, view it on GitHub https://github.com/CredibilityLab/groundhog/issues/112#issuecomment-1911663725, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPNFIJDQOPEDXTBNAYUTCLYQNSRRAVCNFSM6AAAAABCGY76GSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJRGY3DGNZSGU . You are receiving this because you authored the thread.Message ID: @.***>
--
Dr Jennifer Border (*née* Taylor) Senior Research Ecologist
British Trust for Ornithology, The Nunnery, Thetford, Norfolk IP24 2PU Tel: +44 (0) 1842 750050 Fax: +44 (0) 1842 750030 Email: jennifer.border @bto.org @.***>
Registered Charity Number 216652 (England & Wales), SC039193 (Scotland). Company Limited by Guarantee Number 357284 (England and Wales).
urisohn
commented
7 months ago OK looking for way around this. I wonder if channeling the request through another server will do the trick.
From your browser, could you confirm that this URL still doesn't work for you, http://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip
(I would expect it to still not work)
and check whether this alternative URL does work (it should lead to downloading the zip file) https://groundhogr.com/get_file.php?file=windows/4.2/2022-05-06/lme4_1.1-29.zip
urisohn
commented
7 months ago based on issue #113 i now think your issue may be related to GRAN having been an http rather than https site. That's been addressed, could you check if https://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip works for you?
btojenniferborder
commented
7 months ago Hi,
Sorry for the lte reply, this got lost in my inbox. Both of those URL's work fine and so does the other one you sent.
Thanks! Jenni
On Sun, 28 Jan 2024 at 20:55, Uri Simonsohn @.***> wrote:
OK looking for way around this. I wonder if channeling the request through another server will do the trick.
From your browser, could you confirm that this URL still doesn't work for you, http://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip
(I would expect it to still not work)
and check whether this alternative URL does work (it should lead to downloading the zip file)
https://groundhogr.com/get_file.php?file=windows/4.2/2022-05-06/lme4_1.1-29.zip
— Reply to this email directly, view it on GitHub https://github.com/CredibilityLab/groundhog/issues/112#issuecomment-1913719321, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPNFIN2W5YQFX3CZ222QVDYQ23NVAVCNFSM6AAAAABCGY76GSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTG4YTSMZSGE . You are receiving this because you authored the thread.Message ID: @.***>
--
Dr Jennifer Border (*née* Taylor) Senior Research Ecologist
British Trust for Ornithology, The Nunnery, Thetford, Norfolk IP24 2PU Tel: +44 (0) 1842 750050 Fax: +44 (0) 1842 750030 Email: jennifer.border @bto.org @.***>
Registered Charity Number 216652 (England & Wales), SC039193 (Scotland). Company Limited by Guarantee Number 357284 (England and Wales).
HI,
This package was working for me but now i'm getting the following error message:
groundhog.library(c("glmmTMB", "Matrix", "lme4"), "2022-05-14") Will now download 2 packages from GRAN The 2 packages will be downloaded simultaneously in a single batch http://gran.groundhogr.com/windows/4.2/2022-05-06/lme4_1.1-29.zip http://gran.groundhogr.com/windows/4.2/2022-05-06/Matrix_1.4-1.zip Error in utils::download.file(url.split[[bk]], zip.split[[bk]], quiet = TRUE, : cannot download any files Error in if (size_in_bytes < 1024) { : missing value where TRUE/FALSE needed
I can't find any information on how to solve this, any ideas?
Thanks!