Closed isaactpetersen closed 4 years ago
kevinushey
commented
4 years ago It's very surprising to me that snapshotSources() is attempting to build packages. Could you try something like the following:
install.packages("rlang")
trace(packrat:::system_check, quote(print(rlang::trace_back())))and print the stack trace you see associated with the failed build call?
isaactpetersen
commented
4 years ago The package installation worked fine. Here's the trace I get from the second command:
> trace(packrat:::system_check, quote(print(rlang::trace_back())))
Tracing function "system_check" in package "packrat (not-exported)"
[1] "system_check"Sorry -- after running that, please attempt to call packrat::snapshot(). You should see extra debug output after that.
isaactpetersen
commented
4 years ago Here's the output when trying packrat::snapshot():
> packrat::snapshot()
Adding these packages to packrat:
_
RcppEigen 0.3.3.7.0
TeachingDemos 2.12
boot 1.3-24
codetools 0.2-16
crosstalk 1.1.0.1
fastmap 1.0.1
htmlwidgets 1.5.1
httpuv 1.5.4
later 1.1.0.1
lazyeval 0.2.2
lme4 1.1-21
logspline 2.1.16
manipulateWidget 0.10.1
maptools 1.0-1
miniUI 0.1.1.1
minqa 1.2.4
nloptr 1.2.2.1
png 0.1-7
promises 1.1.1
rgl 0.100.54
shiny 1.4.0.2
sourcetools 0.1.7
sp 1.4-2
tcltk2 1.2-11
tkrplot 0.0-24
webshot 0.5.2
xtable 1.8-4
Upgrading these packages already present in packrat:
from to
rlang 0.4.5 0.4.7
Fetching sources for RcppEigen (0.3.3.7.0) ... Tracing system_check(r_path, options, c(r_env_vars(), env_vars), ...) on entry
█
1. └─packrat::snapshot()
2. └─packrat:::snapshotImpl(...)
3. └─packrat:::snapshotSources(project, activeRepos(project), allRecordsFlat)
4. └─base::lapply(...)
5. └─packrat:::FUN(X[[i]], ...)
6. ├─base::try(...)
7. │ └─base::tryCatch(...)
8. │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
9. │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
11. └─packrat:::getSourceForPkgRecord(...)
12. └─(function() {...
13. └─packrat:::build(...)
14. ├─packrat:::with_libpaths(...)
15. │ └─base::force(code)
16. └─packrat:::R(cmd, path, quiet = quiet)
17. ├─packrat:::in_dir(...)
18. │ └─base::force(code)
19. └─packrat:::system_check(...)
Fetching sources for rlang (0.4.7) ... OK (CRAN current)
Fetching sources for RcppEigen (0.3.3.7.0) ... Tracing system_check(r_path, options, c(r_env_vars(), env_vars), ...) on entry
█
1. └─packrat::snapshot()
2. └─packrat:::snapshotImpl(...)
3. └─packrat:::snapshotSources(project, activeRepos(project), allRecordsFlat)
4. └─base::lapply(...)
5. └─packrat:::FUN(X[[i]], ...)
6. ├─base::try(...)
7. │ └─base::tryCatch(...)
8. │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
9. │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
11. └─packrat:::getSourceForPkgRecord(...)
12. └─(function() {...
13. └─packrat:::build(...)
14. ├─packrat:::with_libpaths(...)
15. │ └─base::force(code)
16. └─packrat:::R(cmd, path, quiet = quiet)
17. ├─packrat:::in_dir(...)
18. │ └─base::force(code)
19. └─packrat:::system_check(...)
Error in snapshotSources(project, activeRepos(project), allRecordsFlat) :
Errors occurred when fetching source files:
Error : Command failed (1)
Failed to run system command:
'/opt/ssoft/apps/2020.1/linux-centos7-sandybridge/gcc-9.2.0/r-3.6.2-qzhhzyx/rlib/R/bin/R' --vanilla CMD build '/Users/itpetersen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen' --no-manual --no-resave-data --no-build-vignettes
The command failed with output:
* checking for file '/Users/itpetersen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/DESCRIPTION' ... OK
* preparing 'RcppEigen':
* checking DESCRIPTION meta-information ... OK
Warning in file(con, "r") :
cannot open file 'man': No such file or directory
ERROR
computing Rd index failed:cannot open the connection
Error : Command failed (1)
Failed to run system command:
'/opt/ssoft/apps/2020.1/linux-centos7-sandybridge/gcc-9.2.0/r-3.6.2-qzhhzyx/rlib/R/bin/R' --vanilla CMD build '/Users/itpetersen/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen' --no-manual --no-resave-data --no-build-vignettes
The command failed with outpu
> traceback()
4: stop("Errors occurred when fetching source files:\n", errors)
3: snapshotSources(project, activeRepos(project), allRecordsFlat)
2: snapshotImpl(project, available, lib.loc, dry.run, ignore.stale = ignore.stale,
prompt = prompt && !dry.run, snapshot.sources = snapshot.sources,
infer.dependencies = infer.dependencies)Thanks -- I think I better understand what's going on now.
It looks like Packrat is treating your library directory as a "source" for installed packages, and is trying to build RcppEigen from "sources" as contained in that directory. That attempt is failing, because binaries are installed in the library paths, not sources.
I think the simplest fix would be to use:
packrat::snapshot(snapshot.sources = FALSE)to tell Packrat to create the lockfile without attempting to pre-gather source package tarballs.
isaactpetersen
commented
4 years ago That worked, thank you! I'm new to packrat, so I greatly appreciate your help and your development of the package.
Thanks for developing the wonderful packrat package. I'm using packrat version 0.5.0 in R 3.6.2 on a cluster. I get the following error when using
packrat::snapshot():Here's the traceback:
Thanks in advance!