[Rd] Suggested Patch: Library returns matching installed packages when typo present
Dear R-core devs,
I hope this email finds you well.
Please see the proposed patch to R-devel below:
Scenario:
When loading a package using `library`, a package may not be found if the cases
are not matching:
```
> library(ORG.Hs.eg.db)
Error in library(ORG.Hs.eg.db) :
there is no package called 'ORG.Hs.eg.db'
```
Suggested Patch:
Returns a message matching what `install.packages` returns in such situations:
```
> library("ORG.Hs.eg.db")
Error in library("ORG.Hs.eg.db") :
there is no package called 'ORG.Hs.eg.db'
In addition: Warning message:
Perhaps you meant 'org.Hs.eg.db' ?
```
This patch will be helpful with 'fat-finger' typos. It will match a package
called with `library` against installed packages.
svn diff:
Index: src/library/base/R/library.R
===
--- src/library/base/R/library.R(revision 76727)
+++ src/library/base/R/library.R(working copy)
@@ -300,8 +300,13 @@
pkgpath <- find.package(package, lib.loc, quiet = TRUE,
verbose = verbose)
if(length(pkgpath) == 0L) {
-if(length(lib.loc) && !logical.return)
+if(length(lib.loc) && !logical.return) {
+allpkgs <- .packages(TRUE, lib.loc)
+if (!is.na(w <- match(tolower(package), tolower(allpkgs
+warning(sprintf("Perhaps you meant %s ?",
+sQuote(allpkgs[w])), call. = FALSE, domain = NA)
stop(packageNotFoundError(package, lib.loc, sys.call()))
+}
txt <- if(length(lib.loc))
gettextf("there is no package called %s", sQuote(package))
else
Thank you!
Best regards,
Marcel
--
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Care Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
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Re: [R-pkg-devel] access is denied
I have not had much luck doing package development on network drives. Try using a local drive. On June 20, 2019 11:26:42 AM CDT, Tomas Kalibera wrote: >If you have not already done so, I'd check the package directory (and >its parent) is not opened in any application, including Windows >Explorer, including current working directory in any command prompt. >I'd >also make sure the package is not loaded in any R session. The error >message may be caused by that the file or directory is locked. > >Best >Tomas > >On 6/20/19 5:49 PM, Dennis Boos wrote: >> Developers, >> >> I recently was successful getting a package into CRAN with your help. >> But now I'm working on a second package and am stuck immediately. >Here >> is what I have done. >> >> 1. Created the base package using >http://r-pkgs.had.co.nz/package.html >> to get started. >> 2. Then >> >>> library(devtools) > document() Updating fsr documentation First time >> using roxygen2. Upgrading automatically... Error in >> normalizePath(path.expand(path), winslash, mustWork) : >> >path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": >> Access is denied In addition: Warning messages: 1: In >> normalizePath(path.expand(path), winslash, mustWork) : >> >path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": >> Access is denied 2: In normalizePath(path.expand(path), winslash, >> mustWork) : >> >path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr/DESCRIPTION": >> Access is denied >> >> >> What am I missing? I didn't have this problem before. I have >> re-downloaded RStudio and Rtools, but get the same results. >> >> Dennis >> > >__ >R-package-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] access is denied
If you have not already done so, I'd check the package directory (and its parent) is not opened in any application, including Windows Explorer, including current working directory in any command prompt. I'd also make sure the package is not loaded in any R session. The error message may be caused by that the file or directory is locked. Best Tomas On 6/20/19 5:49 PM, Dennis Boos wrote: Developers, I recently was successful getting a package into CRAN with your help. But now I'm working on a second package and am stuck immediately. Here is what I have done. 1. Created the base package using http://r-pkgs.had.co.nz/package.html to get started. 2. Then library(devtools) > document() Updating fsr documentation First time using roxygen2. Upgrading automatically... Error in normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": Access is denied In addition: Warning messages: 1: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": Access is denied 2: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr/DESCRIPTION": Access is denied What am I missing? I didn't have this problem before. I have re-downloaded RStudio and Rtools, but get the same results. Dennis __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] access is denied
Developers, I recently was successful getting a package into CRAN with your help. But now I'm working on a second package and am stuck immediately. Here is what I have done. 1. Created the base package using http://r-pkgs.had.co.nz/package.html to get started. 2. Then > library(devtools) > document() Updating fsr documentation First time using roxygen2. Upgrading automatically... Error in normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": Access is denied In addition: Warning messages: 1: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr": Access is denied 2: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\wolftech.ad.ncsu.edu\cos\stat\Redirect\boos\Documents\srcis\fsr.package\fsr/DESCRIPTION": Access is denied What am I missing? I didn't have this problem before. I have re-downloaded RStudio and Rtools, but get the same results. Dennis -- Dennis Boos, Assoc. Heademail: dennis_b...@ncsu.edu Department of StatisticsPhone: 919-515-1918 NC State University Fax: 919-515-1169 Raleigh, NC 27695-8203 http://www4.stat.ncsu.edu/~boos Aim for kindness, tolerance, and humility. The rest of life will then fall into place. [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] base::format adds extraneous whitespace for some inputs
> Sarah Goslee > on Thu, 20 Jun 2019 09:56:44 -0400 writes: > I can reproduce this. > It has to do with whether the value rounds down to 9 or up to 10, and > thus needs another space, I think. I agree that it shouldn't happen, > but at least you can get rid of the space by using trim = TRUE. > # rounds to 9 vs 10 > format(9.95, digits = 2) > format(9.96, digits = 2) > format(9.95, digits = 2, nsmall = 2) > format(9.96, digits = 2, nsmall = 2) > format(9.95, digits = 2, nsmall = 2, trim=TRUE) > format(9.96, digits = 2, nsmall = 2, trim=TRUE) > # rounds to 99 vs 100 > format(99.94, digits = 3) > format(99.95, digits = 3) > format(99.94, digits = 3, nsmall = 2) > format(99.95, digits = 3, nsmall = 2) > format(99.94, digits = 3, nsmall = 2, trim=TRUE) > format(99.95, digits = 3, nsmall = 2, trim=TRUE) Yes, indeed; I had wanted to reply earlier, but did not get to. I agree that this is bogous; I've never encountered it as I've (almost?) never used 'nsmall' consciously. Interestingly, this behavior has probably existed unchanged for close to R's full history. The 'nsmall = *' optional argument (of format.default() to be precise) was introduced in R 1.3.0 in 2001. And in my still working version of R 1.3.1, behavior seems similar (not identical) I think. You can access the underlying computations using format.info() from the R level. It calls into the C code which is really used here from the .Internal(format(...)) C code : e.g. > format.info(9.91, 2, 2) [1] 4 2 0 ==> result will use 4 characters > format.info(9.99, 2, 2) [1] 5 2 0 ==> result will use 5 characters - One more thing: format() has really been designed (in S, and inherited for R) to format *several* numbers, often matrices (or data frames if you must) to be printed and look nicely. For this (in cases like these, with numbers), format() must find a common format for all numbers, and that is the reason the underlying algorithm is quite sophisticated because it needs to cover many border line cases, notably deciding on when exponential format is needed, etc etc. For format()ting simple numbers (i.e. numeric vectors of length *one*), using formatC() (or even sprintf() is typically faster and easier to use--for sprintf() you need to know C-standard formatting a bit. >> sessionInfo() > R version 3.5.3 (2019-03-11) > Platform: x86_64-redhat-linux-gnu (64-bit) > Running under: Fedora 28 (Workstation Edition) .. >> # rounds to 9 vs 10 >> >> format(9.95, digits = 2) > [1] "9.9" >> format(9.96, digits = 2) > [1] "10" >> >> format(9.95, digits = 2, nsmall = 2) > [1] "9.95" >> format(9.96, digits = 2, nsmall = 2) > [1] " 9.96" >> >> format(9.95, digits = 2, nsmall = 2, trim=TRUE) > [1] "9.95" >> format(9.96, digits = 2, nsmall = 2, trim=TRUE) > [1] "9.96" >> >> # rounds to 99 vs 100 >> >> format(99.94, digits = 3) > [1] "99.9" >> format(99.95, digits = 3) > [1] "100" >> >> format(99.94, digits = 3, nsmall = 2) > [1] "99.94" >> format(99.95, digits = 3, nsmall = 2) > [1] " 99.95" >> >> format(99.94, digits = 3, nsmall = 2, trim=TRUE) > [1] "99.94" >> format(99.95, digits = 3, nsmall = 2, trim=TRUE) > [1] "99.95" > On Thu, Jun 20, 2019 at 3:19 AM David J. Birke wrote: >> >> Dear R Core Team, >> >> First of all, thank you for your amazing work on developing and >> maintaining this wonderful language. >> >> I just stumbled upon the following behavior in R version 3.6.0: >> >> format(9.91, digits = 2, nsmall = 2) >> format(9.99, digits = 2, nsmall = 2) >> >> yield "9.91" and " 9.99" with an extraneous whitespace. >> >> My expected output for the second command is "9.99". >> >> I have not found anything explaining the whitespace in the help files. >> Therefore, I am writing to report this behavior as a possible bug. >> >> Best wishes, >> David >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > -- > Sarah Goslee (she/her) > http://www.numberwright.com > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] base::format adds extraneous whitespace for some inputs
I can reproduce this. It has to do with whether the value rounds down to 9 or up to 10, and thus needs another space, I think. I agree that it shouldn't happen, but at least you can get rid of the space by using trim = TRUE. # rounds to 9 vs 10 format(9.95, digits = 2) format(9.96, digits = 2) format(9.95, digits = 2, nsmall = 2) format(9.96, digits = 2, nsmall = 2) format(9.95, digits = 2, nsmall = 2, trim=TRUE) format(9.96, digits = 2, nsmall = 2, trim=TRUE) # rounds to 99 vs 100 format(99.94, digits = 3) format(99.95, digits = 3) format(99.94, digits = 3, nsmall = 2) format(99.95, digits = 3, nsmall = 2) format(99.94, digits = 3, nsmall = 2, trim=TRUE) format(99.95, digits = 3, nsmall = 2, trim=TRUE) > sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora 28 (Workstation Edition) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] colorout_1.2-0 loaded via a namespace (and not attached): [1] compiler_3.5.3 tools_3.5.3 > # rounds to 9 vs 10 > > format(9.95, digits = 2) [1] "9.9" > format(9.96, digits = 2) [1] "10" > > format(9.95, digits = 2, nsmall = 2) [1] "9.95" > format(9.96, digits = 2, nsmall = 2) [1] " 9.96" > > format(9.95, digits = 2, nsmall = 2, trim=TRUE) [1] "9.95" > format(9.96, digits = 2, nsmall = 2, trim=TRUE) [1] "9.96" > > # rounds to 99 vs 100 > > format(99.94, digits = 3) [1] "99.9" > format(99.95, digits = 3) [1] "100" > > format(99.94, digits = 3, nsmall = 2) [1] "99.94" > format(99.95, digits = 3, nsmall = 2) [1] " 99.95" > > format(99.94, digits = 3, nsmall = 2, trim=TRUE) [1] "99.94" > format(99.95, digits = 3, nsmall = 2, trim=TRUE) [1] "99.95" On Thu, Jun 20, 2019 at 3:19 AM David J. Birke wrote: > > Dear R Core Team, > > First of all, thank you for your amazing work on developing and > maintaining this wonderful language. > > I just stumbled upon the following behavior in R version 3.6.0: > > format(9.91, digits = 2, nsmall = 2) > format(9.99, digits = 2, nsmall = 2) > > yield "9.91" and " 9.99" with an extraneous whitespace. > > My expected output for the second command is "9.99". > > I have not found anything explaining the whitespace in the help files. > Therefore, I am writing to report this behavior as a possible bug. > > Best wishes, > David > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Sarah Goslee (she/her) http://www.numberwright.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] base::format adds extraneous whitespace for some inputs
Dear R Core Team, First of all, thank you for your amazing work on developing and maintaining this wonderful language. I just stumbled upon the following behavior in R version 3.6.0: format(9.91, digits = 2, nsmall = 2) format(9.99, digits = 2, nsmall = 2) yield "9.91" and " 9.99" with an extraneous whitespace. My expected output for the second command is "9.99". I have not found anything explaining the whitespace in the help files. Therefore, I am writing to report this behavior as a possible bug. Best wishes, David __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
