[Rd] problem with normalizePath()
The packages "readxl" and "haven" (and possibly others) no longer access files
on shared network drives. The problem appears to be in the normalizePath()
function. The file can be read from a local drive or by functions that don't
call normalizePath(). The error thrown is
Error: path[1]="\\Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls": The system
cannot find the file specified
Here's my session:
library(readxl)
library(XLConnect)
# attempting to read file from network drive
df1 <- read_excel("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls")
# pathname is fully qualified, but error thrown as above
cat(normalizePath("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls"))
# throws same error
# reading same file with different function
df2 <- readWorksheetFromFile("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls", 1)
# completes successfully
# reading same file from local drive
df3 <- read_excel("C:/17.xls")
# completes successfully
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_0.1.1 dplyr_0.5.0 XLConnect_0.2-12
[4] XLConnectJars_0.2-12 ROracle_1.2-1DBI_0.5-1
loaded via a namespace (and not attached):
[1] magrittr_1.5 R6_2.2.0 assertthat_0.1 tools_3.3.2haven_1.0.0
[6] tibble_1.2 Rcpp_0.12.7rJava_0.9-8
Please advise.
Thanks,
Michael Laviolette PhD MPH
Public Health Statistician
Bureau of Public Health Statistics and Informatics
New Hampshire Division of Public Health Services
29 Hazen Drive
Concord, NH 03301-6504
Phone: 603-271-5688
Fax: 603-271-7623
Email: michael.laviole...@dhhs.nh.gov
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Re: [Rd] new function to tools/utils package: dependencies based on DESCRIPTION file
Hi Michael,
Are you willing to accept patch for this? I'm already using this and
few related functions for a while, it plays well. I could wrap it as
patch to utils, or tools?
Best,
Jan
On 16 June 2016 at 14:00, Michael Lawrence wrote:
> I agree that the utils package needs some improvements related to
> this, and hope to make them eventually. This type of feedback is very
> helpful.
>
> Thanks,
> Michael
>
>
>
> On Thu, Jun 16, 2016 at 1:42 AM, Jan Górecki wrote:
>> Dear Joris,
>>
>> So it does looks like the proposed function makes a lot sense then, isn't it?
>>
>> Cheers,
>> Jan
>>
>> On 16 June 2016 at 08:37, Joris Meys wrote:
>>> Dear Jan,
>>>
>>> It is unavoidable to have OS and R dependencies for devtools. The building
>>> process for packages is both OS and R dependent, so devtools has to be too
>>> according to my understanding.
>>>
>>> Cheers
>>> Joris
>>>
>>> On 14 Jun 2016 18:56, "Jan Górecki" wrote:
>>>
>>> Hi Thierry,
>>>
>>> I'm perfectly aware of it. Any idea when devtools would be shipped as
>>> a base R package, or at least recommended package? To actually answer
>>> the problem described in my email.
>>> I have range of useful functions available tools/utils packages which
>>> are shipped together with R. They doesn't require any OS dependencies
>>> or R dependencies, unlike devtools which requires both. Installing
>>> unnecessary OS dependencies and R dependencies just for such a simple
>>> wrapper doesn't seem to be an elegant way to address it, therefore my
>>> proposal to include that simple function in tools, or utils package.
>>>
>>> Regards,
>>> Jan Gorecki
>>>
>>> On 14 June 2016 at 16:17, Thierry Onkelinx wrote:
Dear Jan,
Similar functionality is available in devtools::dev_package_deps()
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no more
than
asking him to perform a post-mortem examination: he may be able to say
what
the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
2016-06-14 16:54 GMT+02:00 Jan Górecki :
>
> Hi all,
>
> Packages tools and utils have a lot of useful stuff for R developers.
> I find one task still not as straightforward as it could. Simply to
> extract dependencies of a package from DESCRIPTION file (before it is
> even installed to library). This would be valuable in automation of CI
> setup in a more meta-data driven way.
> The simple function below, I know it is short and simple, but having
> it to be defined in each CI workflow is a pain, it could be already
> available in tools or utils namespace.
>
> package.dependencies.dcf <- function(file = "DESCRIPTION", which =
> c("Depends","Imports","LinkingTo")) {
> stopifnot(file.exists(file), is.character(which))
> which_all <- c("Depends", "Imports", "LinkingTo", "Suggests",
> "Enhances")
> if (identical(which, "all"))
> which <- which_all
> else if (identical(which, "most"))
> which <- c("Depends", "Imports", "LinkingTo", "Suggests")
> stopifnot(which %in% which_all)
> dcf <- read.dcf(file, which)
> # parse fields
> raw.deps <- unlist(strsplit(dcf[!is.na(dcf)], ",", fixed = TRUE))
> # strip stated dependency version
> deps <- trimws(sapply(strsplit(trimws(raw.deps), "(", fixed =
> TRUE), `[[`, 1L))
> # exclude base R pkgs
> base.pkgs <- c("R", rownames(installed.packages(priority = "base")))
> setdiff(deps, base.pkgs)
> }
>
> This allows to easily install all package dependencies just based on
> DESCRIPTION file, so simplify that in custom CI workflows to:
>
> if (length(pkgs<-package.dependencies.dcf(which="all")))
> install.packages(pkgs)
>
> And would not require to install custom packages or shell scripts.
>
> Regards,
> Jan Gorecki
>
> __
> 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
>>
>> __
>> 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/lis
Re: [Rd] new function to tools/utils package: dependencies based on DESCRIPTION file
Hi Jan,
Thanks for volunteering. You, me, Duncan Murdoch (if interested) and
anyone else who is interested should setup an informal chat. We need
to ensure that the API is right and that it fits in well with other
ongoing efforts.
Michael
On Thu, Nov 17, 2016 at 1:40 PM, Jan Gorecki wrote:
> Hi Michael,
> Are you willing to accept patch for this? I'm already using this and
> few related functions for a while, it plays well. I could wrap it as
> patch to utils, or tools?
> Best,
> Jan
>
> On 16 June 2016 at 14:00, Michael Lawrence wrote:
>> I agree that the utils package needs some improvements related to
>> this, and hope to make them eventually. This type of feedback is very
>> helpful.
>>
>> Thanks,
>> Michael
>>
>>
>>
>> On Thu, Jun 16, 2016 at 1:42 AM, Jan Górecki wrote:
>>> Dear Joris,
>>>
>>> So it does looks like the proposed function makes a lot sense then, isn't
>>> it?
>>>
>>> Cheers,
>>> Jan
>>>
>>> On 16 June 2016 at 08:37, Joris Meys wrote:
Dear Jan,
It is unavoidable to have OS and R dependencies for devtools. The building
process for packages is both OS and R dependent, so devtools has to be too
according to my understanding.
Cheers
Joris
On 14 Jun 2016 18:56, "Jan Górecki" wrote:
Hi Thierry,
I'm perfectly aware of it. Any idea when devtools would be shipped as
a base R package, or at least recommended package? To actually answer
the problem described in my email.
I have range of useful functions available tools/utils packages which
are shipped together with R. They doesn't require any OS dependencies
or R dependencies, unlike devtools which requires both. Installing
unnecessary OS dependencies and R dependencies just for such a simple
wrapper doesn't seem to be an elegant way to address it, therefore my
proposal to include that simple function in tools, or utils package.
Regards,
Jan Gorecki
On 14 June 2016 at 16:17, Thierry Onkelinx
wrote:
> Dear Jan,
>
> Similar functionality is available in devtools::dev_package_deps()
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
>
> To call in the statistician after the experiment is done may be no more
> than
> asking him to perform a post-mortem examination: he may be able to say
> what
> the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
> 2016-06-14 16:54 GMT+02:00 Jan Górecki :
>>
>> Hi all,
>>
>> Packages tools and utils have a lot of useful stuff for R developers.
>> I find one task still not as straightforward as it could. Simply to
>> extract dependencies of a package from DESCRIPTION file (before it is
>> even installed to library). This would be valuable in automation of CI
>> setup in a more meta-data driven way.
>> The simple function below, I know it is short and simple, but having
>> it to be defined in each CI workflow is a pain, it could be already
>> available in tools or utils namespace.
>>
>> package.dependencies.dcf <- function(file = "DESCRIPTION", which =
>> c("Depends","Imports","LinkingTo")) {
>> stopifnot(file.exists(file), is.character(which))
>> which_all <- c("Depends", "Imports", "LinkingTo", "Suggests",
>> "Enhances")
>> if (identical(which, "all"))
>> which <- which_all
>> else if (identical(which, "most"))
>> which <- c("Depends", "Imports", "LinkingTo", "Suggests")
>> stopifnot(which %in% which_all)
>> dcf <- read.dcf(file, which)
>> # parse fields
>> raw.deps <- unlist(strsplit(dcf[!is.na(dcf)], ",", fixed = TRUE))
>> # strip stated dependency version
>> deps <- trimws(sapply(strsplit(trimws(raw.deps), "(", fixed =
>> TRUE), `[[`, 1L))
>> # exclude base R pkgs
>> base.pkgs <- c("R", rownames(installed.packages(priority = "base")))
>> setdiff(deps, base.pkgs)
>> }
>>
>> This allows to easily install all package dependencies just based on
>> DESCRIPTION file, so simplify that in custom CI workflows to:
>>
>> if (length(pkgs<-package.dependencies.dcf(which="all")))
>> install.packages(pkgs)
>>
>> And would not require to install custom packages or shell scripts.
>>
>> Regards,
>> Jan Gorecki
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.eth
Re: [Rd] problem with normalizePath()
I wonder if this could be related to the issue that I submitted to bugzilla
about two months ago? (
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17159)
That is to say, could it be that it's treating the first path after the
single backslash as an actual directory, rather than as the name of the
share?
--
Evan Cortens, PhD
Institutional Analyst - Office of Institutional Analysis
Mount Royal University
403-440-6529
On Thu, Nov 17, 2016 at 2:28 PM, Laviolette, Michael <
michael.laviole...@dhhs.nh.gov> wrote:
> The packages "readxl" and "haven" (and possibly others) no longer access
> files on shared network drives. The problem appears to be in the
> normalizePath() function. The file can be read from a local drive or by
> functions that don't call normalizePath(). The error thrown is
>
> Error: path[1]="\\Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls": The
> system cannot find the file specified
>
> Here's my session:
>
> library(readxl)
> library(XLConnect)
>
> # attempting to read file from network drive
> df1 <- read_excel("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls")
> # pathname is fully qualified, but error thrown as above
>
> cat(normalizePath("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls"))
> # throws same error
>
> # reading same file with different function
> df2 <- readWorksheetFromFile("//Hzndhhsvf2/data/OCPH/EPI/BHSDM/Group/17.xls",
> 1)
> # completes successfully
>
> # reading same file from local drive
> df3 <- read_excel("C:/17.xls")
> # completes successfully
>
> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] readxl_0.1.1 dplyr_0.5.0 XLConnect_0.2-12
> [4] XLConnectJars_0.2-12 ROracle_1.2-1DBI_0.5-1
>
> loaded via a namespace (and not attached):
> [1] magrittr_1.5 R6_2.2.0 assertthat_0.1 tools_3.3.2haven_1.0.0
> [6] tibble_1.2 Rcpp_0.12.7rJava_0.9-8
>
> Please advise.
> Thanks,
>
> Michael Laviolette PhD MPH
> Public Health Statistician
> Bureau of Public Health Statistics and Informatics
> New Hampshire Division of Public Health Services
> 29 Hazen Drive
> Concord, NH 03301-6504
> Phone: 603-271-5688
> Fax: 603-271-7623
> Email: michael.laviole...@dhhs.nh.gov
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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[Rd] R-intro.texi patch
Note, the R-intro.R is correct. svn diff R-intro.texi Index: R-intro.texi === --- R-intro.texi(revision 71664) +++ R-intro.texi(working copy) @@ -1525,7 +1525,7 @@ After this assignment, the standard errors are calculated by @example -> incster <- tapply(incomes, statef, stderr) +> incster <- tapply(incomes, statef, stdError) @end example @noindent Evelyn Mitchell [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
