Package: qmap
Check: examples
New result: ERROR
  Running examples in ‘qmap-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: fitQmapDIST
  > ### Title: Quantile mapping using distribution derived transformations
  > ### Aliases: fitQmapDIST fitQmapDIST.default fitQmapDIST.matrix
  > ###   fitQmapDIST.data.frame doQmapDIST doQmapDIST.default
  > ###   doQmapDIST.matrix doQmapDIST.data.frame
  > 
  > ### ** Examples
  > 
  > data(obsprecip)
  > data(modprecip)
  > 
  > qm.fit <- fitQmapDIST(obsprecip[,1],modprecip[,1],
  +                       distr="berngamma",
  +                       qstep=0.001)
  > qm <- doQmapDIST(modprecip[,1],qm.fit)
  > 
  > 
  > qm.lnorm.fit <- fitQmapDIST(obsprecip[,1],modprecip[,1],
  +                       distr="bernlnorm",
  +                       qstep=0.001)
  Error in fitQmapDIST.default(obsprecip[, 1], modprecip[, 1], distr = "bernlnorm",  : 
    'mledist' failed to estimate parameters for 'mod' with the error code 1
  Calls: fitQmapDIST -> fitQmapDIST.default
  Execution halted

Package: RFlocalfdr
Check: examples
New result: ERROR
  Running examples in ‘RFlocalfdr-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: determine.C
  > ### Title: determine.C
  > ### Aliases: determine.C
  > 
  > ### ** Examples
  > 
  > data(imp20000)                                      
  > imp<-log(imp20000$importances)                               
  > t2<-imp20000$counts
  > temp<-imp[t2 > 1]   #see                          
  > temp<-temp[temp != -Inf]                         
  > temp <- temp - min(temp) + .Machine$double.eps   
  > f_fit <- f.fit(temp)                             
  > y <- f_fit$zh$density                            
  > x <- f_fit$midpoints                             
  > df <- data.frame(x, y)                           
  > initial.estimates <- fit.to.data.set.wrapper(df, temp, try.counter = 3,return.all=FALSE)           
  Warning in cov2cor(varcovar) :
    diag(V) had non-positive or NA entries; the non-finite result may be dubious
  Warning in sqrt(diag(varcovar)) : NaNs produced
  > initial.estimates<-  initial.estimates$Estimate
  Error in initial.estimates$Estimate : 
    $ operator is invalid for atomic vectors
  Execution halted

Package: NA
Check: NA
Old result: NA
New result: NA

Package: Seurat
Check: Rd cross-references
New result: NOTE
  Found the following Rd file(s) with Rd \link{} targets missing package
  anchors:
    CCAIntegration.Rd: DimReduc
    FindNeighbors.Rd: Neighbor, Graph, Graphs
    FindTransferAnchors.Rd: RANN, RcppAnnoy
    IntegrateData.Rd: DimReduc, RANN, Assay
    IntegrateEmbeddings.Rd: DimReduc
    JointPCAIntegration.Rd: DimReduc
    PrepSCTIntegration.Rd: Assay
    RPCAIntegration.Rd: DimReduc
    RunCCA.Rd: merge.Seurat
    SCTAssay-class.Rd: Assay
    TopNeighbors.Rd: Neighbor
    TransferData.Rd: DimReduc, RANN
    fortify-Spatial.Rd: Segmentation-class, Centroids-class,
      Molecules-class
  Please provide package anchors for all Rd \link{} targets not in the
  package itself and the base packages.

Package: stratifyR
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘stratifyR-vignette.Rmd’ using rmarkdown
  ** Processing: /home/hornik/tmp/CRAN_recheck/stratifyR.Rcheck/vign_test/stratifyR/vignettes/stratifyR-vignette_files/figure-html/unnamed-chunk-1-1.png
  768x576 pixels, 8 bits/pixel, 256 colors in palette
  Reducing image to 8 bits/pixel, grayscale
  Input IDAT size = 10482 bytes
  Input file size = 11352 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9216
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9178
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9178
  
  Output IDAT size = 9178 bytes (1304 bytes decrease)
  Output file size = 9256 bytes (2096 bytes = 18.46% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/stratifyR.Rcheck/vign_test/stratifyR/vignettes/stratifyR-vignette_files/figure-html/unnamed-chunk-2-1.png
  768x576 pixels, 8 bits/pixel, 256 colors in palette
  Reducing image to 8 bits/pixel, grayscale
  Input IDAT size = 11568 bytes
  Input file size = 12438 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10144
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10095
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10095
  
  Output IDAT size = 10095 bytes (1473 bytes decrease)
  Output file size = 10173 bytes (2265 bytes = 18.21% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/stratifyR.Rcheck/vign_test/stratifyR/vignettes/stratifyR-vignette_files/figure-html/unnamed-chunk-3-1.png
  768x576 pixels, 8 bits/pixel, 256 colors in palette
  Reducing image to 8 bits/pixel, grayscale
  Input IDAT size = 12104 bytes
  Input file size = 12974 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10889
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10889
  
  Output IDAT size = 10889 bytes (1215 bytes decrease)
  Output file size = 10967 bytes (2007 bytes = 15.47% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/stratifyR.Rcheck/vign_test/stratifyR/vignettes/stratifyR-vignette_files/figure-html/unnamed-chunk-5-1.png
  768x576 pixels, 8 bits/pixel, 256 colors in palette
  Reducing image to 8 bits/pixel, grayscale
  Input IDAT size = 11722 bytes
  Input file size = 12592 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10294
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10234
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10234
  
  Output IDAT size = 10234 bytes (1488 bytes decrease)
  Output file size = 10312 bytes (2280 bytes = 18.11% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/stratifyR.Rcheck/vign_test/stratifyR/vignettes/stratifyR-vignette_files/figure-html/unnamed-chunk-7-1.png
  768x576 pixels, 8 bits/pixel, 256 colors in palette
  Reducing image to 8 bits/pixel, grayscale
  Input IDAT size = 10575 bytes
  Input file size = 11445 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9153
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9128
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9128
  
  Output IDAT size = 9128 bytes (1447 bytes decrease)
  Output file size = 9206 bytes (2239 bytes = 19.56% decrease)
  
  
  Quitting from lines 636-641 [unnamed-chunk-9] (stratifyR-vignette.Rmd)
  Error: processing vignette 'stratifyR-vignette.Rmd' failed with diagnostics:
  subscript out of bounds
  --- failed re-building ‘stratifyR-vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘stratifyR-vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted