* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/dcemriS4.Rcheck’
* using R Under development (unstable) (2020-02-19 r77832)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dcemriS4/DESCRIPTION’ ... OK
* this is package ‘dcemriS4’ version ‘0.55’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dcemriS4’ can be installed ... [15s/40s] 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 R 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [20s/49s] NOTE
.CA.fast2: no visible global function definition for ‘lsfit’
.T2.fast: no visible global function definition for ‘txtProgressBar’
.T2.fast: no visible global function definition for ‘setTxtProgressBar’
.dcemri.bayes: no visible global function definition for ‘median’
.dcemri.bayes: no visible global function definition for ‘sd’
.dcemri.map : posterior: no visible global function definition for
  ‘dnorm’
.dcemri.map : posterior: no visible global function definition for
  ‘dgamma’
.dcemri.map : posterior: no visible global function definition for
  ‘dbeta’
.dcemri.map.single: no visible global function definition for ‘optim’
.dcemri.spline: no visible binding for global variable ‘median’
.dcemri.spline: no visible global function definition for ‘median’
.dcemri.spline.single: no visible binding for global variable
  ‘quantile’
.dcemri.spline.single: no visible binding for global variable ‘median’
.dcemri.spline.single: no visible global function definition for
  ‘median’
.ftm: no visible global function definition for ‘fft’
.ftm: no visible global function definition for ‘matplot’
.ftm: no visible global function definition for ‘legend’
compartmentalModel : <anonymous>: no visible global function definition
  for ‘approx’
convFFT: no visible global function definition for ‘fft’
extractAIF : c.start: no visible global function definition for ‘sd’
extractAIF : c.start: no visible global function definition for ‘cor’
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘dcemriS4/libs/dcemriS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/53s] OK
* checking differences from ‘dcemriS4-Ex.Rout’ to ‘dcemriS4-Ex.Rout.save’ ... OK

2c2
< oro.nifti 0.10.1
---
> oro.nifti 0.5.2
67c67
< 37.14845803  3.89506170  1.51615801 -0.01066008 
---
> 37.14845917  3.89506144  1.51615753 -0.01066018 
223c223
< [1] 1.522074
---
> [1] 1.522075
226c226
< [1] -0.00983221
---
> [1] -0.00983213
248,260c248,260
<  [1,] 0.145599052 0.1678452 0.16592766 0.55254849
<  [2,] 0.218344559 0.2658134 0.24219283 0.50264588
<  [3,] 0.250521815 0.3129245 0.27084876 0.48798627
<  [4,] 0.268391926 0.3403433 0.28533489 0.48014076
<  [5,] 0.279725126 0.3582433 0.29400920 0.47516094
<  [6,] 0.009912791 0.7331255 0.01475737 0.09028427
<  [7,] 0.146992146 0.2043296 0.15691602 0.47338401
<  [8,] 0.328712966 0.3961533 0.36284044 0.49722427
<  [9,] 0.387767110 0.4608153 0.43840557 0.50468089
< [10,] 0.250521815 0.2491542 0.24915417 0.45785051
< [11,] 0.250521815 0.2801023 0.25820501 0.47252745
< [12,] 0.250521815 0.3476498 0.28871475 0.50510375
< [13,] 0.250521815 0.3833826 0.31198211 0.52406079
---
>  [1,] 0.145599052 0.1678452 0.16592766 0.55254848
>  [2,] 0.218344559 0.2658134 0.24219283 0.50264587
>  [3,] 0.250521815 0.3129245 0.27084876 0.48798626
>  [4,] 0.268391926 0.3403433 0.28533489 0.48014075
>  [5,] 0.279725126 0.3582433 0.29400920 0.47516093
>  [6,] 0.009912791 0.7331255 0.01475737 0.09028433
>  [7,] 0.146992146 0.2043296 0.15691602 0.47338402
>  [8,] 0.328712966 0.3961533 0.36284044 0.49722426
>  [9,] 0.387767110 0.4608153 0.43840557 0.50468088
> [10,] 0.250521815 0.2491542 0.24915417 0.45785050
> [11,] 0.250521815 0.2801023 0.25820501 0.47252744
> [12,] 0.250521815 0.3476498 0.28871475 0.50510374
> [13,] 0.250521815 0.3833826 0.31198211 0.52406078
272c272
<  [1,] 0.0600 1.840405e-03 1.371417e-03
---
>  [1,] 0.0600 1.840405e-03 1.371419e-03
274c274
<  [3,] 0.0600 2.818906e-02 2.771863e-02
---
>  [3,] 0.0600 2.818906e-02 2.771864e-02
278,279c278,279
<  [7,] 0.0600 3.971422e-02 3.895468e-02
<  [8,] 0.0600 1.899215e-02 1.873550e-02
---
>  [7,] 0.0600 3.971422e-02 3.895469e-02
>  [8,] 0.0600 1.899215e-02 1.873551e-02
281c281
< [10,] 0.0001 1.128817e-17 3.025228e-18
---
> [10,] 0.0001 1.128817e-17 3.025355e-18
333c333
<  [6,] 0.02202843 2.2508666 2.2508260 2.2398360 2.2396892
---
>  [6,] 0.02202843 2.2508666 2.2509156 2.2398360 2.2396892
349c349
<  [6,] 0.009912791 0.5241719 0.5241635 0.5221588 0.5221473
---
>  [6,] 0.009912791 0.5241719 0.5241820 0.5221588 0.5221473
522c522
< 99.5197734  0.6534572 
---
> 99.5197735  0.6534572 
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 [4s/10s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [21s/41s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/dcemriS4.Rcheck/00check.log’
for details.


Time 5:18.25, 122.87 + 9.94