##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zFPKM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zFPKM_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/zFPKM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zFPKM/DESCRIPTION’ ... OK
* this is package ‘zFPKM’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zFPKM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotGaussianFitDF: no visible global function definition for ‘dnorm’
PlotGaussianFitDF: no visible binding for global variable ‘density’
PlotGaussianFitDF: no visible binding for global variable ‘log2fpkm’
PlotGaussianFitDF: no visible binding for global variable ‘sample_name’
zFPKMCalc: no visible global function definition for ‘density’
zFPKMTransform: no visible global function definition for ‘is’
Undefined global functions or variables:
  density dnorm is log2fpkm sample_name
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "density", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘zFPKM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: zFPKM
> ### Title: zFPKM Transformation
> ### Aliases: zFPKM
> ### Keywords: zFPKM
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz"
> temp <- tempfile()
> download.file(gse94802, temp)
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz'
Warning in download.file(gse94802, temp) :
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz': FTP status was '550 Requested action not taken; file unavailable'
Error in download.file(gse94802, temp) : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz'
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/zFPKM.Rcheck/00check.log’
for details.