I am trying to make a for-loop with a function pathway that prints a png in the current directory. The i is rownames in paths.hsa.my. My example below did not yield anything, please see the error below.
library("pathview")
for(i in rownames(paths.hsa.my)){
pathview(inn.m[,1],pathway.id = "i",species = "hsa")
}
head of my input:
head(rownames(paths.hsa.my))
[1] "hsa00010" "hsa00020" "hsa00030" "hsa00040" "hsa00051" "hsa00052"
Here is my error:
Warning: Failed to download KEGG xml/png files, hsai skipped!
Info: Downloading xml files for hsai, 1/1 pathways..
Warning: Download of hsai xml file failed!
This pathway may not exist!
Related
Are there any workarounds to the problem with ncdf4::nc_open not being able to access some .nc files from a URL? I would like to avoid having to download the file first since this is for a shiny app deployed on a server and so I want to avoid users being able to download files to the server.
Some URLs work e.g. this OPeNDAP URL from a THREDDS server:
library(ncdf4)
nc <- nc_open("https://dapds00.nci.org.au/thredds/dodsC/uc0/Test_pixel_count.nc")
But others do not e.g. this NetCDF Subset Service URL from a THREDDS server:
nc <- nc_open("https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1")
# Error in nc_open("https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1") :
# Error in nc_open trying to open file https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1
or this file directly from a website:
nc <- nc_open("https://www.unidata.ucar.edu/software/netcdf/examples/ECMWF_ERA-40_subset.nc")
# syntax error, unexpected WORD_WORD, expecting SCAN_ATTR or SCAN_DATASET or SCAN_ERROR
# context: <!DOCTYPE^ HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"><html><head><title>404 Not Found</title></head><body><h1>Not Found</h1><p>The requested URL was not found on this server.</p></body></html>
# Error in R_nc4_open: NetCDF: file not found
# Error in nc_open("https://www.unidata.ucar.edu/software/netcdf/examples/ECMWF_ERA-40_subset.nc") :
# Error in nc_open trying to open file https://www.unidata.ucar.edu/software/netcdf/examples/ECMWF_ERA-40_subset.nc
What could be the reason why some methods work and some don't, and are there any ways to fix this?
I ran into the same issue and contacted the creator of ncdf4. Here is his reply:
The ncdf4 R package is an interface to the underlying netcdf library on your machine. The R package cannot avoid limitations or problems with the netcdf library itself. You can always see how the underlying netcdf library handles a URL by just trying to use "ncdump" with the URL. For example,
% ncdump "https://dapds00.nci.org.au/thredds/dodsC/uc0/Test_pixel_count.nc"
Gives:
netcdf Test_pixel_count {
dimensions:
lat = 283 ;
lon = 451 ;
variables:
byte crs ;
crs:_Unsigned = "false" ;
crs:grid_mapping_name = "latitude_longitude" ;
crs:long_name = "CRS definition" ;
crs:longitude_of_prime_meridian = 0. ;
crs:semi_major_axis = 6378137. ;
crs:inverse_flattening = 298.257222101 ;
crs:spatial_ref = "GEOGCS[\"GEOCENTRIC DATUM of AUSTRALIA\",DATUM[\"GDA94\",SPHEROID[\"GRS80\",6378137,298.257222101]],PRIMEM[\"Greenwich\",0],UNIT[\"degree\",0.0174532925199433],AXIS[\"Longitude\",EAST],AXIS[\"Latitude\",NORTH]]" ;
crs:GeoTransform = "141.4607205456306 0.0075 0 -22.95189554231917 0 -0.0075 " ;
etc. I.e., the netcdf library itself can read this URL/file.
However when I do this:
% ncdump "https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1"
I get this error:
ncdump "https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1"
ncdump: https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1: https://dapds00.nci.org.au/thredds/ncss/uc0/Test_pixel_count.nc?var=Band1&north=-22.9556&west=142&east=143&south=-25.0706&disableProjSubset=on&horizStride=1:
NetCDF: Malformed or unexpected Constraint
So the netcdf library itself cannot access that URL/file, and therefore ncdf4 cannot do so. There's not anything I would be able to do to the ncdf4 library to make up for this.
You might try contacting the netcdf library folks and ask if this is expected behavior or a bug.
I need the data of the .rdata file for text mining. These are my dataset. I don't know exactly what's in that file. The problem is i can't load it.
I tried to open the file with different windows computers but with the same errors. I used RStudio in the updated version. I google the error-Information but nothing worked. Because I can open other rdata files there should be no registry problem. I wanted to check in an other basic windows Editor to look what is in the file but there were only signs like: ‹ ìùuPo³6
’#p ÜÝ‚»»»[pw—…»»»»»†àînÁuA°E`!‡ßûîýí}æÌLMÕÌùæŸÝõTñÈ}÷ÝrõÕ½
¢hXˆ
I tried different possibilities to open the file in RStudio with different error informations as followed:
with load()
require("readr")
setwd("C:/Users/..")
options(stringsAsFactors = F)
load("file")
# Error in load("file") :
# bad restore file magic number (file may be corrupted) -- no data loaded
# In addition: Warning message:
# file ‘.rdata’ has magic number ''
# Use of save versions prior to 2 is deprecated
with source()
require("readr")
setwd("C:/Users/..")
options(stringsAsFactors = F)
source("file")
# Error in source("file") :
# file.rdata:1:1: unexpected input
# 1:
# ^
readRDS
setwd("C:/Users/..")
options(stringsAsFactors = F)
readRDS("file")
# Error in readRDS("file") : unknown input format
I've faced a problem with saving plotly diagram p as html file, when the filename name is not in English:
htmlwidgets::saveWidget(p, paste0(name, "_all.html"))
For English filenames it works just fine, but when name variable contains Russian characters it fails with error:
pandoc.exe: Could not fetch 28%E1_all_files/htmlwidgets-0.9/htmlwidgets.js
28пїЅ_all_files/htmlwidgets-0.9/htmlwidgets.js: openBinaryFile:
does not exist (No such file or directory)
Error: pandoc document conversion failed with error 67
In this example
> name
[1] "28б"
Is there a way to fix that problem?
Thank You very much.
I have installed the required packages - gdata and ggplot2 and I have installed perl.
library(gdata)
library(ggplot2)
# Read the data from the excel spreadsheet
df = data.frame(read.xls ("AssignmentData.xlsx", sheet = "Data", header = TRUE, perl = "C:\\Strawberry\\perl\\bin\\perl.exe"))
However when I run this I get the following error:
Error in xls2sep(xls, sheet, verbose = verbose, ..., method = method, :
Intermediate file 'C:\Users\CLAIRE~1\AppData\Local\Temp\RtmpE3UYWA\file8983d8e1efc.csv' missing!
In addition: Warning message:
running command '"C:\STRAWB~1\perl\bin\perl.exe" "C:/Users/Claire1992/Documents/R/win-library/3.1/gdata/perl/xls2csv.pl" "AssignmentData.xlsx" "C:\Users\CLAIRE~1\AppData\Local\Temp\RtmpE3UYWA\file8983d8e1efc.csv" "Data"' had status 2
Error in file.exists(tfn) : invalid 'file' argument
Thanks to #Stibu I realised I had to set my work directory. This is the command you use to run in Rstudio; setwd("C/Documents..."). The file path is where the excel file is located.
I had the issue but I solved it differently.
My problem was because my file was saved as Excel (extension .xls) but it was a txt file.
I corrected the file and I did not meet any other error with the R function.
I'm trying to reproduce the example for tex2docx function in reports R package and getting the following error.
DOC <- system.file("extdata/doc_library/apa6.qual_tex/doc.tex",
package = "reports")
BIB <- system.file("extdata/docs/example.bib", package = "reports")
tex2docx(DOC, file.path(getwd(), "test.docx"), path = NULL, bib.loc = BIB)
Error Message
pandoc.exe: Error reading bibliography `C:/Users/Muhammad'
citeproc: the format of the bibliographic database could not be recognized
using the file extension.
docx file generated!
Warning message:
running command 'C:\Users\MUHAMM~1\AppData\Local\Pandoc\pandoc.exe -s C:/Users/Muhammad Yaseen/R/win-library/3.0/reports/extdata/doc_library/apa6.qual_tex/doc.tex -o C:/Users/Muhammad Yaseen/Documents/test.docx --bibliography=C:/Users/Muhammad Yaseen/R/win-library/3.0/reports/extdata/docs/example.bib' had status 23
I wonder how to get tex2docx function in reports R package working properly.
As described in the above comments, the error is caused by passing a filename/path including some spaces that are nor escaped, nor quoted. A workaround could be wrapping all file paths and names inside of shQuote before passing to the command line with system.
Code: https://github.com/trinker/reports/pull/31
Demo:
Loading package
library(reports)
Creating a dummy dir with a space in the name that would hold the bib file
dir.create('foo bar')
file.copy(system.file("extdata/docs/example.bib", package = "reports"), 'foo bar/example.bib')
Specifying the source and the copied bib file:
DOC <- system.file("extdata/doc_library/apa6.qual_tex/doc.tex", package = "reports")
BIB <- 'foo bar/example.bib'
Running the test:
tex2docx(DOC, file.path(getwd(), "test2.docx"), path = NULL, bib.loc = BIB)
Disclaimer: I tried to test this pull request, but I could not setup an environment with all the needed tools to run R CMD check with vignettes and everything else after all in 5 mins (sorry but being on vacation right now and just enjoying the siesta after lunch), so please consider this pull request as "untested" -- although it should work.